text:
Why are Gram points for the Riemann zeta important?

Given the Riemann-Siegel function, why are the Gram points important? I say if we have $S(T)$, the oscillating part of the zeros, then given a Gram point and the imaginary part of the zeros (under the Riemann Hypothesis), are the Gram points near the imaginary part of the Riemann zeros?

I say that if the difference $|\gamma _{n}- g_{n} |$ is regulated by the imaginary part of the Riemann zeros.

-
If you don't start accepting answers, people just won't help you. –  sxd Nov 12 '11 at 14:05
but in comments there are not thick mark for votes :) .. whenever they gave a question i click on the thick mark if possible i will review all the answers given and will vote again. –  Jose Garcia Nov 13 '11 at 11:33
This is not about comments. You can upvote comments, but you can't accept them (and people don't get reputation for upvotes to their comments). It's about accepting one of the answers to your question. Answers and comments are two separate things. Answers are the things underneath where it says "$n$ Answers:". Comments are the things in small print underneath the question and the answers. –  joriki Nov 13 '11 at 15:01

One thing Gram points are good for is that they help in bracketing/locating the nontrivial zeroes of the Riemann $\zeta$ function.

More precisely, recall the Riemann-Siegel decomposition

$$\zeta\left(\frac12+it\right)=Z(t)\exp(-i\;\vartheta(t))$$

where $Z(t)$ and $\vartheta(t)$ are Riemann-Siegel functions.

$Z(t)$ is an important function for the task of finding nontrivial zeroes of the Riemann $\zeta$ function, in the course of of verifying the hypothesis. (See also this answer.)

That is to say, if some $t_k$ satisfies $Z(t_k)=0$, then $\zeta\left(\frac12+it_k\right)=0$.

Now, Gram points $\xi_k$ are numbers that satisfy the relation $\vartheta(\xi_k)=k\pi$ for some integer $k$. They come up in the context of "Gram's law", which states that $(-1)^k Z(\xi_k)$ tends to be positive. More crudely, we can say that Gram points tend to bracket the roots of the Riemann-Siegel function $Z(t)$ (i.e. there is often a root of $Z(t)$ in between consecutive $\xi_k$):

"Gram's law" doesn't always hold, however:

There are a number of other "bad" Gram points.

-


text:
# Talk:Harmonia Nectere Passus

## Back to page

14,874pages on
this wiki

Just wondered, would it be too speculative to expand from "Harmonia Nectere Passus perfects a Vanishing Cabinet's performance" to "Harmonia Nectere Passus binds broken bonds and magical connections, such as those of a Vanishing Cabinet's, hence improving their performance"? -- 13:16, February 24, 2013 (UTC)

I don't know-- do we have any direct evidence that this was the spell's effect on the cabinet? ProfessorTofty (talk) 04:31, March 8, 2013 (UTC)
Not really, except the etymology section of the article. So I suppose that's a no-go? I mean, it does seem a logical assumption in my opinion (hence my posting here) but all the same, there's no canon to support it. 12:09, March 8, 2013 (UTC)
If there's no canon, then I'm afraid that's a no. I looked at the etymology section, too, and I didn't really see enough information in my opinion to justify that conclusion. The truth is, we don't really know enough about exactly how the Vanishing Cabinet was broken, only that Malfoy was trying desperately to fix it. ProfessorTofty (talk) 13:29, March 8, 2013 (UTC)

format: plain


text:
...a decent amount of equations on the radio, they don't sound sexy. so when I say like, umm, Einstein's theory of relativity is E=mc^2, that, that's not enticing. So we're gonna see if Tom Hiddleston could make these sound a little bit more enticing. I'm gonna add some dramatic reverb. If you could do it to that camera there, this could really, I mean you could help people win at whatever equations [that] falls under us. Everyone, now I'm revising your equations. Here's how they go: Einstein's theory of relativity is, E=mc^2. This means that energy, equals mass times the speed of light, squared. The Pythagorean equation, is, A^2 + B^2= C^2. This means that for all right angle triangles, the square on the hypotenuse is equal to the sum of the squares on the other 2 sides. How am I doing? Is this, I mean, it's really educational, and slightly erotic. This is the last one: Pi, is the circumference divided by the diameter of any circle. It's impossible to know the exact value, but pi is approximately 3.14159265358979328462 Oh beautiful stuff! Yes, I mean, that is, that really really was quite something.

# 【Tom Hiddleston】史上最性感的數學課：抖森教你畢氏定理！根本無法專心啊！(Tom Hiddleston Makes Maths Sexy!)

35063
Kristi Yang 發佈於 2018 年 12 月 21 日

1. ## 1. 單字查詢

在字幕上選取單字即可即時查詢單字喔！

2. ## 2. 單句重複播放

可重複聽取一句單句，加強聽力！

3. ## 3. 使用快速鍵

使用影片快速鍵，讓學習更有效率！

4. ## 4. 關閉語言字幕

進階版練習可關閉字幕純聽英文哦！

5. ## 5. 內嵌播放器

可以將英文字幕學習播放器內嵌到部落格等地方喔

6. ## 6. 展開播放器

可隱藏右方全文及字典欄位，觀看影片更舒適！

1. ## 英文聽力測驗

挑戰字幕英文聽力測驗！

1. 點擊展開筆記本讓你看的更舒服

1. UrbanDictionary 俚語字典整合查詢。一般字典查詢不到你滿意的解譯，不妨使用「俚語字典」，或許會讓你有滿意的答案喔


text:
# Find all complex numbers satisfying |z+3+4i|=|z-5|

Find all complex numbers satisfying
$|z+3+4i|=|z-5|$
You can still ask an expert for help

• Questions are typically answered in as fast as 30 minutes

Solve your problem for the price of one coffee

• Math expert for every subject
• Pay only if we can solve it

Jacob Homer
Step 1
$|z+3+4i|=|z-5|$
Let $z=z+iy$
So $|\left(x+3\right)+i\left(y+4\right)|=|\left(x-5\right)+iy|$
$\sqrt{{\left(x+3\right)}^{2}+{\left(y+4\right)}^{2}}=\sqrt{{\left(x-5\right)}^{2}+{y}^{2}}$
${x}^{2}+9+6x+{y}^{2}+16+8y={x}^{2}+25-10x+{y}^{2}$
$16x+8y=0$
$wx+y=0$
$y=-2x$
So $z=x-2i$
$z=x\left(1-2i\right)$
Ex $x=1⇒z=1-2i$
$x=2⇒z=2-4i$
$z=3⇒z=3-6i$


text:
# Regarding some econometric problems

How do I know the specification in (3.2) is a chi-square distribution with df k-1? and why is it the case that the asymptotic variance of $$\hat{\beta}_{FD}- \hat{\beta}_{OLS}$$ is simply the difference of asymptotic variance of $$\hat\beta_{FD}$$ and that of $$\hat\beta_{OLS}$$?

*FD refers to first-difference method

Could someone help me with it? Still struggling figuring it out. Many thanks.

The following is the material from William H. Greene's Econometric analysis 7th edition, p.379

• I think most of the answers to your question are here: en.wikipedia.org/wiki/Durbin%E2%80%93Wu%E2%80%93Hausman_test – Andrew M Jun 2 '19 at 14:05
• Two things to clarify: (i) What is $k$? (ii) What does $\hat{avar}$ mean? About (i), in (3.2), $k-1$ is supposed to be the rank of the avar matrix. For (ii), it looks like $\hat{avar}$ is the estimated asymptotic variance of $\sqrt{nT}$ times the argument. Regarding your last question, "$avar(a-b) = avar(a)-avar(b)$" is the heart of Hausman's finding, where $b$ is an efficient estimator. – chan1142 Jun 2 '19 at 14:30
• First of all, I want to thank you both for answering me, especially when I'm new to this platform. And I would like to clarify that in the context of my question, k refers to the number of variables in the regression model, with the constant included, while avar hat refers to the estimated asymptotic variance of square root of nT multiplied by the argument mentioned in the question, which is to be used when performing Hausman test. – Jeff Jun 3 '19 at 3:37
• As from the the wiki page describing the Hausman test, I've checked, but confused. For this reason, I read William H. Greene's Econometric analysis 7th edition, p.379, in which Hausman test is performed to determine whether to adopt random effect or fixed effect method, to see if it helps. What I find out is that the author of the book also mentioned the heart of Hausman's finding, the covariance of an efficient estimator with its difference from an inefficient estimator is zero. In this sense, "b" should be an inefficient estimator one, right? – Jeff Jun 3 '19 at 4:13
• Also, by comparing the results shown in Greene's book and the wiki page, I just failed to connect the concepts conveyed in both sides. Namely, in the covariance matrix of the difference vector, which estimator should be the first one? Efficient or inefficient one? In the variance part of the wald statistic, the order should be the same as the the covariance matrix of the difference vector, but it turns out not the case in the wiki page? – Jeff Jun 3 '19 at 4:42

The first screenshot (reference?) assumes that OLS is efficient when $$\alpha_i=0$$ for all $$i$$. That is, it is assumed that the idiosyncratic errors are $$iid$$ so OLS achieves asymptotic efficiency under the null hypothesis. Let $$(\hat\alpha_{ols}, \hat\beta_{ols}')'$$ be the OLS estimator, where the dimension of $$\hat\beta_{ols}$$ is $$k-1$$. Then Hausman's results imply that $$avar(\hat\beta_{fd} - \hat\beta_{ols}) = avar(\hat\beta_{fd}) - avar(\hat\beta_{ols}).$$ [Algebra is given in Greene's textbook. You shouldn't switch the order of the RHS terms as it should be positive semidefinite.] Note that $$avar(\hat\beta_{fd} - \hat\beta_{ols}) = avar(\hat\beta_{ols} - \hat\beta_{fd})$$ so it does not matter which one comes first. The key implication of Hausman's result is that the variance of the difference equals the difference of the variances (if one is efficient). The result that $$nT (\hat\beta_{fd} - \hat\beta_{ols})' \hat{avar}(\hat\beta_{fd} - \hat\beta_{ols})^{-1} (\hat\beta_{fd} - \hat\beta_{ols}) \to \chi^2_{k-1}$$ is rather straightforward because the dimension of $$\hat\beta$$'s is $$(k-1)\times 1$$. [If $$\xi_n \to N(0, C)$$, where $$\xi_n$$ is $$m\times 1$$, then $$\xi_n' \hat{C}^{-1} \xi_n \to_d \chi^2_{m}$$, where $$\hat{C}$$ is a consistent estimator of $$C$$.] The $$nT$$ factor is there because $$avar(z)$$ is the asymptotic variance of $$\sqrt{nT}$$ times $$z$$.

Hausman's test is a general tool, which can be used for any efficient estimator. In your original question, OLS is efficient (because it is assumed so by the author of the document though it is not clearly stated so) so Hausman's test can be used for the comparison of an inefficient estimator (FD) and an efficient estimator (OLS). In the RE/FE testing, RE is efficient by assumption so Hausman's test can be used. There are lots of other examples of Hausman tests.

BTW, the assumption that the idiosyncratic errors are $$iid$$, which is generally required for the efficiency of OLS or RE, is very strong, and is not satisfied by typical panel applications. For the panel model $$y_{it} = \alpha_i + x_{it}\beta + e_{it}$$, where $$x_{it}$$ is strictly exogenous, $$e_{it}$$ represents factors other than time-invariant factors ($$\alpha_i$$) and $$x_{it}$$. I see no strong reasons why $$e_{it}$$ should be serially independent. (This is similar to a time-series model with strictly exogenous regressors. The Newey-West (heteroskedasticity and autocorrelation consistent) estimator is developed to handle this case.) The Hausman test using OLS and FD is based on the strong assumption that there is no heteroskedasticity or autocorrelation in $$e_{it}$$. If $$e_{it}$$ is serially correlated or heteroskedastic, OLS is not efficient under the null hypothesis that $$\alpha_i$$ is constant, and the mentioned Hausman test fails.

Simlarly, the Hausman test of RE vs FE relies on the efficiency of RE, which again requires that $$e_{it}$$ is $$iid$$ (loosely speaking). But again there are no strong reasons why $$e_{it}$$ should be so. (It's different for dynamic models which require serial independence for identification.)

• Thank you for great insight on my question, you really help me a lot. But just one last question. I understand the fact that Hausman's heart finding is that the covariance of an efficient estimator with its difference from an inefficient estimator is zero, and the algebra is given in the textbook, but how to interpret it intuitively in plain language. Is it just because it look simpler without having to take into consideration of the interaction terms? – Jeff Jun 5 '19 at 14:53
• In Hausman's original paper published in 1978, he mentioned that if an efficient estimator is correlated with its difference from an inefficient estimator, then a linear combination of an efficient estimator and its difference from an inefficient estimator would lead to an unbiased estimator, say beta star, which would have smaller variance than the originally assumed efficient estimator. What does this imply? How do I convince a friend who does not know Hausman well that this finding is so important that it is Hausman's heart finding? – Jeff Jun 5 '19 at 15:02
• Many thanks again! – Jeff Jun 5 '19 at 15:02
• What my concern here is that I may be able to show the algebra, the derivation, and tell people from the textbook I know this part is Hausman's heart finding, but can't interpret anything more than this. – Jeff Jun 5 '19 at 15:20
• You seem to be interested in intuitively understanding Hausman’s result. I think your second comment on Hausman (1978) is nice. If $a$ and $b-a$ are correlated, then $a+h\times (b-a)$ should have a smaller variance than $a$ for some $h$. In order for $a$ to be efficient, $a$ and $b-a$ should be uncorrelated. – chan1142 Jun 5 '19 at 15:52


text:
# Regarding the state of our chat room

Our chat room, the Observatory, has existed for almost 10 years, yet it doesn't have many messages in it. On average these days, one message is posted every week, mainly regarding interesting ramblings in the science world and links to other questions.

Our chat room needs more love, but what can we (and the rest of the community) do to keep our chat room alive (and not sputtering with random, intermittent messages)?

• All it takes is interest really. Unfortunately our userbase hasn't really had interest in a long time, but there hadn't been any interest in meta for a while either and it's picked back up, so you never know!
– called2voyage Mod
Apr 13, 2021 at 14:02
• @called2voyage If only moderators could add in "site-exclusive" badges... Participation in chat would be a big one... Apr 13, 2021 at 14:32
– called2voyage Mod
Apr 13, 2021 at 14:33
• @called2voyage Yes, but these don't really provide a valuable incentive for users (there could be more) Apr 13, 2021 at 14:34
• If you have ideas for more you could always propose them on MSE. They may be useful to more than just Astro.
– called2voyage Mod
Apr 13, 2021 at 14:35
• But I'm not really sure badges are actually helpful in this case. Of the two we have, only 25 have earned the bronze one and just a handful have earned the silver one.
– called2voyage Mod
Apr 13, 2021 at 14:38
• My biggest problem is that I did keep forgetting how to find the chat - I knew it existed whenever the discussions in comments gets lengthy, but the link directing there is not too prominent nor intuitive. Apr 21, 2021 at 10:49
• There's a chat room? Who knew?! Apr 24, 2021 at 13:50

When it comes to chat, I think it's best to keep to an organic "If you build it, they will come"$$^{\dagger}$$ type of approach. It was always meant to be a third place, but not everyone wants or needs that - and that's fine! I personally don't use the Observatory that often because my day is centered around astronomy, and when I have free time - well, I'm usually using that free time to do something totally unrelated. Given that we have a number of full-time astronomers among the most active users, I wouldn't be surprised if others feel the same way.

Participation in chat doesn't necessarily lead to community growth; rather, I'd argue that it's instead a byproduct of that. A bigger userbase means more folks who might be interested in using chat. Therefore, I think that it's not worth trying to artificially stimulate chat room usage. If there were issues with the culture of the chat room - violations of SE rules, rude language, unwelcoming attitudes, etc. - well, that would probably warrant a thorough meta discussion. But that's definitely not the case.

$$^{\dagger}$$I know it's actually "he", not "they", but . . . eh.

• Definitely agree
– called2voyage Mod
Apr 14, 2021 at 18:16

There are several high quality science/math/tech SE sites with excellent, mature and active user communities and yet nearly zero activity in their general chat rooms.

Chat is for "disposable" discussion, it scrolls off, is hard to search, and is generally forgotten. It really is a place to chat and if users aren't the chatty type or have found much better places to chat, then the room will naturally be quiet.

Our chat room needs more love,

As I see it there is no problem to be addressed, if love is needed it's in maintaining tags, answering questions, being kind and helpful to new users, giving them advice and sometimes just editing their posts rather than insta-closing them.

• I am happy to have matter-based discussion as (semi-persistents) comments, and not in a somewhat hidden chat room. But that's just my view. Apr 21, 2021 at 10:48


text:
Home | Form | Analytic | Tax |

# find an invertible matrix p and a matrix c of the form

## This image has been removed at the request of its copyright owner

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text:
complex mean-value theorem

Theorem [1] Suppose $\Omega$ is an open convex set in $\mathbb{C}$, suppose $f$ is a holomorphic function $f:\Omega\to\mathbb{C}$, and suppose $a,b$ are distinct points in $\Omega$. Then there exist points $u,v$ on $L_{ab}$ (the straight line connecting $a$ and $b$ not containing the endpoints), such that

 $\displaystyle\Re\{\frac{f(b)-f(a)}{b-a}\}=\Re\{f^{\prime}(u)\},$ $\displaystyle\Im\{\frac{f(b)-f(a)}{b-a}\}=\Im\{f^{\prime}(v)\},$

where $\Re$ and $\Im$ are the real (http://planetmath.org/RealPart) and imaginary parts of a complex number, respectively.

References

• 1 J.-Cl. Evard, F. Jafari, A Complex Rolle’s Theorem, American Mathematical Monthly, Vol. 99, Issue 9, (Nov. 1992), pp. 858-861.
Title complex mean-value theorem ComplexMeanvalueTheorem 2013-03-22 13:49:02 2013-03-22 13:49:02 matte (1858) matte (1858) 7 matte (1858) Theorem msc 26A06


text:
Combine the fastq files
0
0
Entering edit mode
3.0 years ago

Hello,

I have four whole genome sequencing data files which two files are reverse and two files forward, Right? (Attached in the image):

I want to map these files using the bwa software to the reference genome. Should i combine two reverse files together, and also combine two forward files together? If I should combine, which files should I combine (According to the picture)? And what command line should I use for combine?

Or no need to combine? How to map them to the reference genome?

SNP • 1.8k views
0
Entering edit mode

I am not sure why someone chose to change the R1/R2 nomenclature for read files to L1/L2 but you can combine R1 files together and R2 files together. You can't do them by clicking on the names in that view you have of some GUI. You will have to do that on the command line by using cat R1_file1.fq.gz R1_file2.fq.gz > R1_one.fq.gz.

Aligning them in pieces and then combining the resulting BAM file is a valid option too.

0
Entering edit mode

I expect L1/L2 are lanes (renamed from L001 and L002, though I haven't a clue whey they did that).

0
Entering edit mode

For my samples combine L1_1/L1_2 together and L2_1/L2_2 together, Right?

0
Entering edit mode

If what @Devon says is right i.e. L1_1is actually L001_R1 and L2_1 is L002_R1 then you would combine L1_1 with L2_1. Then L1_2 with L2_2.

0
Entering edit mode

Since these are not fasta files based on their names, I edited the title of the post to accurately reflect file type.

Also see: mapping form different lane

0
Entering edit mode

If you want to do variant calling with GATK (maybe other tools?), it is important to map them separately and add relevant read group information to each file.

0
Entering edit mode

Is there a lane component to the read group?

1
Entering edit mode

Yes and no (and take into account I barely did variant calling, my knowledge is second-hand). Lane is a possible source of technical variation, so if the information is present, it is used for base recalibration. One can add lane using the PU flag. Even if you don't add the PU flag, one should make the RG flag unique for same sample on different lanes. Here is a snippet from the GATK forum:

PU = Platform Unit

The PU holds three types of information, the {FLOWCELL_BARCODE}.{LANE}.{SAMPLE_BARCODE}. The {FLOWCELL_BARCODE} refers to the unique identifier for a particular flow cell. The {LANE} indicates the lane of the flow cell and the {SAMPLE_BARCODE} is a sample/library-specific identifier. Although the PU is not required by GATK but takes precedence over ID for base recalibration if it is present. In the example shown earlier, two read group fields, ID and PU, appropriately differentiate flow cell lane, marked by .2, a factor that contributes to batch effects.

0
Entering edit mode

Thanks. I wonder how relevant this is these days. Do people even do base recalibration anymore? I too haven't done much in the way of variant calling lately, in case you can't tell :)

0
Entering edit mode

yes, i want to use GATK for variant calling. So, should I now map each file separately to the reference genome? I do not understand exactly what you mean? Or, in other words, I do not know exactly which files I want to map first?

Is this my command line correct?

for L1_1/L2_1 :

bwa mem -t 12 -M -R "@RG\tID: BBKHU01_F\tLB: BBKHU01_ F\tPL:ILLUMINA\tSM: BBKHU01_F" /home/m.rafiepour222/GCF_000471725.1_UMD_CASPUR_WB_2.0_genomic.fa /home/m.rafiepour222/BBKHU01_F/BBKHU01_F_D17073416_H353KDMXX_L1_1.clean.fq.gz /home/m.rafiepour222/BBKHU01_F/BBKHU01_F_D17073416_H353KDMXX_L2_1.clean.fq.gz > BBKHU01_F.sam_1

and for L1_2/L2_2 :

bwa mem -t 12 -M -R "@RG\tID: BBKHU01_F\tLB: BBKHU01_ F\tPL:ILLUMINA\tSM: BBKHU01_F" /home/m.rafiepour222/GCF_000471725.1_UMD_CASPUR_WB_2.0_genomic.fa /home/m.rafiepour222/BBKHU01_F/BBKHU01_F_D17073416_H353KDMXX_L1_2.clean.fq.gz /home/m.rafiepour222/BBKHU01_F/BBKHU01_F_D17073416_H353KDMXX_L2_2.clean.fq.gz > BBKHU01_F.sam_1

If it is not correct, please tell me which command line should I use?

0
Entering edit mode

Ok, So i once map L1_1 / L2_1 into the reference genome and once again L1_2 / L2_2, Just like the command line you edited for me , right?

Then convert the output of each step in the SAM file to the BAM file and then combine the two BAM files together? Am I correct?


text:
# 0.1.1 - Order of Operations

The acronym PEMDAS, or the mnemonic "please excuse my dear aunt Sally," are sometimes used to help students remember the basic order of operations, where P = parentheses, E = exponents (and square roots), M = multiplication, D = division, A = addition, and S = subtraction.

When performing a series of mathematical operations, begin inside the parentheses. Next, calculate any exponents or square roots. Then, multiplication and division. And finally, addition and subtraction. For a more in-depth review, we recommend the Khan Academy's Order of Operations lesson.

In this course, we will be using fractions often. When working with fractions, you can imagine that the operations in the numerator are within parentheses and the operations in the denominator are in parentheses. Below are a few examples of mathematical operations that will be applied in this course. We'll learn about the applications of these operations later in the course, here, we're focusing only on the mathematical operations.

## Example: Confidence Interval for a Mean Section

A confidence interval for a mean can be computed using the equation $$\bar x \pm SE (t^*)$$. Let's construct a confidence interval given $$\bar x = 5.770$$, $$SE = 0.335$$, and $$t^* = 2.080$$.

First, we'll plug in the given values.

$$5.770 \pm 0.355(2.080)$$

There are no operations within parentheses and no exponents or square roots, so our next step will be to multiply.

$$5.770 \pm 0.697$$

The symbol ± tells use to both subtract and add.

$$5.770 - 0.697 = 5.073$$

$$5.770 + 0.697 = 6.467$$

The confidence interval is (5.073, 6.467).

## Example: Test Statistic for a Proportion Section

A test statistic for a one sample proportion hypothesis test can be computed using the equation $$z = \frac {\hat p - p_0}{\sqrt{\frac{p_0 (1-p_0)}{n}}}$$. Let's work through this formula using the following values: $$\hat p = 0.87$$, $$p_0 = 0.8$$, and $$n=100$$.

First, we'll plug in the given values.

$$z = \frac {0.87 - 0.8}{\sqrt{\frac{0.8 (1- 0.8)}{100}}}$$

In the first few steps we'll work in the numerator and denominator separately. Let's start in the numerator, which contains only subtraction.

$$z = \frac {0.07}{\sqrt{\frac{0.8 (1- 0.8)}{100}}}$$

Next, let's focus on the denominator. The operation within the parentheses should be conducted first.

$$z = \frac {0.07}{\sqrt{\frac{0.8 (0.2)}{100}}}$$

Within the denominator, we can work within the top of the fraction first,

$$z = \frac {0.07}{\sqrt{\frac{0.16}{100}}}$$

Solve for fraction under the square root in the denominator.

$$z = \frac {0.07}{\sqrt{0.0016}}$$

Next, take the square root in the denominator.

$$z = \frac {0.07}{0.04}$$

And finally, divide the numerator by the denominator.

$$z = 1.75$$


text:
## What is the most correct way to run a program? It's not so obvious!

Get help with using AutoHotkey and its commands and hotkeys
john_c
Posts: 174
Joined: 05 May 2017, 13:19

### What is the most correct way to run a program? It's not so obvious!

The question seems to be very easy, but it's not so obvious.

For example, try to press Win+1 without AutoHotkey. What will you see? As soon as you pressed it, the first program from taskbar will be launched.

And here is simple script for it:

; This:F1:: SendInput, #1; Or this:F1:: #1

But with script, the behavior is different. If you keep F1 pressed, instead of quickly release it, the application will be launched multiple times.

Here is another way, with KeyWait command:

F1:: KeyWait, F1 SendInput, #1Return

It will fix the issue with multiple launches, but introduces another issue - the program will be launched when F1 released, instead of pressed. So, the behavior is different from default Windows behavior (still).

Probably there exists some another, more robust way of launching programs?

I don't mean launching from taskbar, though. It was just an example. Here is another example, which is more close to real life:

F1:: Run, C:\foo\bar\some_program.exe
Last edited by john_c on 16 Sep 2018, 07:11, edited 1 time in total.
lexikos
Posts: 6129
Joined: 30 Sep 2013, 04:07
GitHub: Lexikos

### Re: What is the most correct way to run a program? It's not so obvious!

The correct way to run a program is to run the program, as you've done at the end of your post.

Your problem has very little to do with running the program. Your problem is that you expect the hotkey's action to execute only once each time you press and release the key, which does not align with how keyboard keys work. If you don't want a key's function to repeat while you hold it down, you can turn off key-repeat. Otherwise, you should expect this behaviour and work around it on a case-by-case basis.

Most likely the solution you're after is to simply put KeyWait, F1 after SendInput, #1.

But with script, the behavior is different. If you keep F1 pressed, instead of quickly release it, the application will be launched multiple times.
Different to what? It is consistent with standard Windows 10 behaviour. If I hold #1, it will repeatedly launch that application for each time the key repeats.
john_c
Posts: 174
Joined: 05 May 2017, 13:19

### Re: What is the most correct way to run a program? It's not so obvious!

Most likely the solution you're after is to simply put KeyWait, F1 after SendInput, #1.

Thanks! Yes, it seems to work correctly! Isn't it a best practice to always use KeyWait before last Return?

Different to what? It is consistent with standard Windows 10 behaviour. If I hold #1, it will repeatedly launch that application for each time the key repeats.

Hm. I use Win7. In Win 7, the application will be launched each time you press Win+1. But if you press it only once and then continue keep your fingers on buttons, the application will not be launched repeatedly - it will be launched just once. With AutoHotkey, if we keep fingers on buttons for some time (e.g. 5 seconds), the application will be launched again and again (if we don't use KeyWait).
lexikos
Posts: 6129
Joined: 30 Sep 2013, 04:07
GitHub: Lexikos

### Re: What is the most correct way to run a program? It's not so obvious!

john_c wrote:Isn't it a best practice to always use KeyWait before last Return?
It isn't "best practice". It is common sense. If you put a command after return, the command will not execute, because the subroutine has already returned.

Otherwise, you put KeyWait at whatever point you want the script to wait. Whether you do so before or after performing some other action has no impact on whether key-repeat triggers the hotkey. Key-repeats are ignored because the hotkey hasn't returned yet, which is because it is still waiting.
DRocks
Posts: 89
Joined: 08 May 2018, 10:20

### Re: What is the most correct way to run a program? It's not so obvious!

Interesting!

Then what is the difference, please, with using something like F11 UP:: ?

Would F11 UP:: be too drastic compared to F11:: KeyWait F11... ?

Edit: I am thinking about this with a context in the back of my head: im trying with Wolf_II to script the best possible Edit control that only takes Numbers, 1 dot, two decimals, etc. We found that interception of keys before they are typed is better than String manipulations.

So,
To limit key repeat im using the key UP option... and then also a inStr check to valide presence or absence of a Dot in the edit control. If there is one it return rather than trigerring on key UP.

Do you think that this is valid and logical or that KeyWait is more appropriate?
lexikos
Posts: 6129
Joined: 30 Sep 2013, 04:07
GitHub: Lexikos

### Re: What is the most correct way to run a program? It's not so obvious!

john_c wrote:Isn't it a best practice to always use KeyWait before last Return?
I realize I may have misinterpreted the question; that the emphasis may have been on always using KeyWait, and not on where to place it ("before last Return"). It is not best practice to block key-repeat. However, if you want to do it, KeyWait is the easiest way.

DRocks wrote:Then what is the difference, please, with using something like F11 UP:: ?
Putting KeyWait before the action, as john_c did, has a similar effect to a key-up hotkey. If you had paid attention to the topic, you would see that this effect was not desired.
john_c wrote:introduces another issue - the program will be launched when F1 released, instead of pressed.

There's nothing "drastic" about an up-hotkey. If you want to perform some action only when the key is released, it is the best way. john_c did not want to perform some action when the key was released, so an up-hotkey was not appropriate. As for your own script, that is a separate topic.

Off-topic: If you are creating the Edit control, it is not appropriate to use hotkeys, which rely on global registration or a system-wide hook. Use OnMessage to monitor WM_KEYDOWN and related messages.
john_c
Posts: 174
Joined: 05 May 2017, 13:19

### Re: What is the most correct way to run a program? It's not so obvious!

Cross-link to related thread: Prevent hotkey from repeating
john_c
Posts: 174
Joined: 05 May 2017, 13:19

### Re: What is the most correct way to run a program? It's not so obvious!

DRocks wrote:Then what is the difference, please, with using something like F11 UP:: ? Do you think that this is valid and logical or that KeyWait is more appropriate?

Hi! I'm just newbie.

Notice the difference:

1st example: SendInput will be launched when you RELEASE the button. It's NOT how Windows works by default:

F1 Up:: SendInput, FooReturn

2nd example: SendInput will be launched when you PRESS the button. This is exactly how Windows works by default. So, from UX-centric point of view it seems to be better:

F1:: SendInput, Foo KeyWait, F1Return
Last edited by john_c on 16 Sep 2018, 06:41, edited 4 times in total.
john_c
Posts: 174
Joined: 05 May 2017, 13:19

### Re: What is the most correct way to run a program? It's not so obvious!

lexikos wrote:I realize I may have misinterpreted the question; that the emphasis may have been on always using KeyWait, and not on where to place it ("before last Return"). It is not best practice to block key-repeat. However, if you want to do it, KeyWait is the easiest way.

Thanks! Yes, it was exactly what I asked for! :)
DRocks
Posts: 89
Joined: 08 May 2018, 10:20

### Re: What is the most correct way to run a program? It's not so obvious!

Thanks to both of you! I get it much better now and am able to make more sense out of it in my mind.

And tha ks for the nice tip Lexikos about the OnMessage being more appropriate. I assume when you interpret "create" the edit control we are both talking about making a Gui, add, edit,.... control right? This is what I meant when I said "create".

Ill investigate on the hint you gave me. Very interesting. Thanks

Édit: ive Made a function Edit OnMessage to do basic stuff so far so good... but its too complex versus AHK building hotkey feature. Il using the #if focused control match Edit_ to only affect keyboard in this context. Is this proper too according to how AHK is made?


text:
These small glass packages have silicon diodes inside. The black band at one end is the cathode, the side where current flows out of the diode.

The diode is our first semiconductor device. A diode’s distinctive feature is that it conducts current in one direction but not in the other. We won’t go into the details of how a diode does this or how it’s made. Fortunately, you don’t have to know how to make a diode before you can use it in a circuit.

Written by Willy McAllister.

### Where we’re headed

• A diode conducts strongly in one direction, and practically $0$ in the other.

• Learn to identify the terminals of a real-world diode – cathode and anode.

• Understand diode terms – forward bias, reverse bias, saturation current, and breakdown.

A diode is any electrical device with the property that it conducts in one direction and not in the opposite direction. Every diode you will come across in modern electronics is made with semiconductor material.

What is a semiconductor?

Semiconductor materials fall between insulators and conductors. They semi-conduct. Semiconductors usually act like insulators, but we can control how much they conduct by changing the way they are made – by adding faint amounts of impurity atoms – and by applying voltage.

The most well-known and well-understood semiconductor material is Silicon (Si, atomic number $14$) in the periodic table. Silicon is by far the most common material used for creating semiconductor devices. More is known about silicon than perhaps any other material on Earth.

Part of the periodic table showing silicon (Si) and other nearby semiconductor materials. B - boron, C - carbon, N - nitrogen, Al - aluminum, Si - silicon, P - phosphorus, Ga - gallium, Ge - germanium, As - arsenic.

Other semiconductor materials include germanium (Ge, atomic number $32$, right below Silicon), and gallium-arsenide, a $1 : 1$ ratio of Gallium and Arsenic, also known as GaAs, (atomic numbers $31$ and $33$, on either side of germanium).

Our ability to finely control the conducting properties of silicon allows us to create modern marvels like computers and mobile phones and every other complex electronic device. The details of how a semiconductor works are governed by quantum mechanics.

## Diode symbol

The schematic symbol for a diode looks like this,

The black arrow ► in the symbol points in the direction of the diode’s forward current, $\blueD i$. The diode’s voltage, $\goldD v$, is oriented with the $+$ sign on the end where forward current comes into the diode, just like the sign convention for passive components.

## Diode terminals

When you draw diodes, the symbol clearly indicates the direction of forward current flow. You usually don’t need names for the two terminals. You will come across them in data sheets, the Anode and Cathode.

### How can I remember the anode and cathode?

For the longest time I could not remember which end of the diode was the anode and which was the cathode – I looked it up every time. I finally came up with a memory aid. The German word for cathode is Kathode. The big K kind of looks like a diode symbol.

Flip the diode symbol around until it reads like a K. The Kathode is the terminal on the left.

### Identify the terminals of a real-world diode

If you are handling real diodes you have to figure out which way to point the diode. Real-world diodes are so small there isn’t room to paint a little diode symbol on them, so you need to identify the terminals some other way.

Diodes come in all sorts of tiny packages. There are a few ways to indicate which diode terminal is which.

Diode packages like the glass and black plastic cylinders shown above usually have a painted bar near one end. The bar on the package is the bar of the diode symbol, so it indicates the cathode.

The stripe (any contrasting color) corresponds to the diode's cathode.

This red LED (light emitting diode) does not have a stripe, but instead has wire leads of different length. The forward current goes into the longer lead (anode). The package may have a bump or tab sticking out on the anode side.

The longer lead corresponds to the anode. Current flow into the diode from this direction.

### Identify the terminals with a multimeter

A reliable way to verify the identity of the terminals is using a multimeter to figure out the forward current direction. When the meter is set to read resistance, $\Omega$, it puts a small voltage on its test leads (this is why an ohm meter needs a battery). You use that small voltage to see which way current flows.

The diode is flipped in each image.

$\text a.$ If the ohmmeter reads a finite resistance that means the diode is conducting a small current in the forward direction. A small current is flowing from the red $+$ lead through the diode. That means the red lead is touching the anode.
$\text b.$ If the resistance reads O.L (for overload), the diode is not conducting current. That means the red $+$ lead is touching the cathode.

Your meter might have a diode setting – a little diode symbol.

If it does, the meter will display the forward voltage and may beep when the red lead is touching the forward current terminal (the anode).

## Types of diodes

There are many types of diodes, differing in materials and processing, and specialized for different uses. Here are a few, (some of these terms haven’t been defined yet)

• Silicon diode – Silicon is the most common material for making diodes. Silicon has a typical forward voltage of $0.6–0.7\,\text V$.
• Germanium diode – Made from a different element. Germanium diodes have a lower forward voltage of $0.25–0.30\,\text V$.
• Schottky diode – Made from direct contact between silicon and metal. The forward voltage is lower than regular silicon diodes, in the range of $0.15$ to $0.45\,\text V$. This is the diode in a “cat whisker” crystal radio.
• Zener diode – Intentionally operated in the breakdown region, used as a voltage reference.
• LED (light-emitting diode) – Does what its name says. Otherwise, it acts like a regular diode with a forward voltage somewhere between $2$ and $4\,\text V$ depending on the color. LEDs are made of materials on either side of Silicon on the periodic table. For example, you can make a yellow LED from gallium arsenide phosphide (GaAsP).
• Photodiode – This diode has a window to let light fall directly on the silicon surface. The current in the diode is proportional to the intensity of light. Solar cells are photodiodes.
• Small signal diode or switching diode – A silicon diode constructed to be very fast changing from forward current to reverse current and back. This is done by making the diode physically very small.

## Diode $i$-$v$ characteristic

A diode is a non-linear device. This is a typical $i$-$v$ curve for a silicon diode,

Diode $i$-$v$ curve of a silicon diode. A positive voltage (anode higher than cathode) on the diode puts it in its forward biased region. A negative voltage means the diode is operating in its reverse biased region. At negative voltages exceeding $\text V_{\text{br}}$ the diode is in breakdown and the current rapidly increases in the negative direction.

The blue curve above can be created by measurements. Take an ordinary diode and apply different voltages to it. Write down the current at each voltage. Your $i$-$v$ data will resemble this plot.

## Forward bias

Let’s say we place a small positive voltage, like $+0.2$ volts, across a silicon diode. That puts us just a little bit to the right of the origin of the $i$-$v$ curve. With this small positive voltage, very little forward current flows. If we increase the voltage up to around $+0.6\,\text V$ a measurable current starts to flow through the diode in the forward direction (in the direction of the arrow ►). As the voltage moves a little above $0.6\,\text V$, the current through the diode rises rapidly. The $i$-$v$ curve is nearly vertical at this point (it tips a little to the right).

With a positive voltage on its terminals, we say the diode is forward biased. A diode is forward biased when its voltage is anywhere on the $+$voltage side of the origin. In normal operation, the voltage across a forward biased silicon diode is somewhere between $0.60–0.75\,\text V$. If you force the voltage higher than $0.75$ volts, the diode current goes way up and it may overheat.

## Reverse bias

If you apply a negative voltage to a diode, so the $-$cathode terminal is higher voltage than the $+$anode terminal, this puts us on the left side of the $i$-$v$ curve. We say the diode is reverse biased. In the reverse direction, the current is very close to zero, just ever so slightly negative.

There is a tiny bit of current that flows when a diode is reverse biased. We call it the reverse saturation current. This current flows in the opposite direction of the arrow ►, from the cathode towards the anode. A well-made diode has a typical reverse current of $10^{-9}$ to $10^{-12}\,\text A$. In most situations, this is close enough to zero to be ignored. In some cases (like an integrated circuit with millions of diodes), the reverse saturation current becomes important and you give it a bad-sounding name: leakage current.

What does "bias" mean?

You hear the word bias in conversations about diodes and transistors. It does not have a single precise definition.

In everyday use, bias can be negative, implying unfairness or favoritism, "The rules are biased against me." Or it might describe a tendency, "They show a bias for taking action." Or "The goalkeeper has a bias for jumping to the left on penalty kicks."

In electronics, bias comes up in only a few situations. It has the sense of pulling towards one side. When talking about diodes as we are doing here, forward bias means an applied voltage is tugging the diode towards the forward conducting side of its $i$-$v$ curve. Reverse bias is the opposite, a negative voltage pulls the diode into its reverse bias region where it does not conduct.

The other place you talk about bias: You apply a bias voltage to the terminals of a transistor to place it in a voltage range where it works best. For example, if a transistor works best when its input terminal is between $1$ and $3$ volts, you apply a bias voltage centered at $2$ volts, right in the middle of its happy zone.

## Reverse breakdown

A reverse biased diode can’t hold out forever. When the voltage reaches a high negative value known as the breakdown voltage, $\text{V}_{\text{br}}$, the diode starts to conduct in the reverse direction. At breakdown, the current sharply increases and becomes very high in the negative direction. A breakdown voltage $\text{V}_\text{br}$ of $-50\,\text V$ is typical of ordinary diodes. Most of the time you don’t allow the diode voltage to get near $\text{V}_\text{br}$.

## Summary

The schematic symbol and terminal names for a diode,

A diode conducts strongly in the direction of the black arrow, and essentially $0$ current can flow in the opposite direction.

A diode made of silicon has a forward voltage between $0.60–0.75\,\text V$.


text:
[–] 1 point2 points  (1 child)

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You picked Voyager 1 because of its distance. But time dilation is an effect on velocity. A corollary to this question may be, what is the fastest man made object that has traveled for a long period of time and what is its time dilation?

[–][S] 0 points1 point  (0 children)

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Interesting. Although I am not sure the increase in velocity is drastic enough to counter the 35 years that Voyager 1 has been traveling. Would be interesting to look into, though. I am not sure on the speeds at which other ships travel.

[–] 1 point2 points  (1 child)

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This begs the question… The Sun is in orbit within the Milky way so it goes around with a given velocity (say Vs), and the Earth, goes around the sun (at, say, Ve).

As the Earth crosses the sun's vector twice a year, it's speed relative to the center of the Milky Way would oscillate between Vs+Ve and Vs-Ve.

Could that velocity difference have an effect on astronomical measurement timings made from the Earth?

[–]Sample Synthesis | Magnetism | Superconductivity 0 points1 point  (0 children)

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astronomical measurement timings

What are you asking? With a few exceptions (like pulsars), every phenomenon we look at outside the solar system is measured in months or years, if not longer.

[–] 0 points1 point  (11 children)

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Negligible. If t is the time that passes on Earth, t' is the time that has passed on Voyager since launch, \delta t'= \gamma \delta t, where \gamma=1/(1-v2 /c2). Assuming the velocity relative to Earth was constant at 16,000 m/s (it wasn't due to gravitational slingshotting) and that it experienced no gravitational time dilation, and given that it has been going for 1.11 x 109 seconds,

\delta t'=t/(1-v2 /c2 ) =(1.11*109 ) /(1-160002 /(2.998x108 )2 )=1.110000003x109 seconds, a 0.0000003% increase. In other words, negligible.

[–][S] 0 points1 point  (10 children)

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The point isn't how negligible is it, it is how much is it. According to facecube, it is a total of 1.62 seconds.

[–] 2 points3 points  (5 children)

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The point isn't how negligible is it, it is how much is it

That's why I worked it out.

According to facecube, it is a total of 1.62 seconds.

I have no idea what a facecube is, but it's wrong. Voyager is going way too slow for the difference to be that big.

[–]Algebra | Analysis 0 points1 point  (4 children)

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facecube is the poster of the (current) top comment. They admitted that the actual difference is far smaller than 1.62 seconds, so they are not necessarily wrong.

[–] -1 points0 points  (3 children)

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Ah, I thought it was some Zynga startup meant to compete with Wolfram Alpha. Nonetheless, my answer is correct, the math is right there.

[–]Sample Synthesis | Magnetism | Superconductivity 1 point2 points  (2 children)

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You have a missing factor of 10. Voyager 1 is about 1.83x1013 m away and has been traveling for about 1.11x109 s, so if we assume it's been traveling in a straight line then its average speed is over 16000m/s, not 1600. I get the same answer as facecube to within 0.05s. Since it has actually traveled farther than that (it hasn't been going in a straight line, especially at the beginning) the path length is actually longer than that and the time difference is bigger than this suggests.

[–] 0 points1 point  (1 child)

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I'd love for somebody who knows more about orbital mechanics than me to make a list of all the factors I ignored. It would be a very long list!

[–]Sample Synthesis | Magnetism | Superconductivity 0 points1 point  (0 children)

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If I had the exact path it followed, it wouldn't be that hard to figure out all the special relativity corrections. The biggest thing is that gamma isn't linear with v/c, so you can't just use the average velocity if you really want accuracy. I also don't know the form of the general relativistic time correction, so I wouldn't be able to account for the effect of the gravitational slingshotting or distance from the sun on that.

[–] 4 points5 points  (2 children)

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It's much much less than 1.62 seconds. It's only 1.62 seconds if you ignore everything else and treat the speed as constant, which it isn't.

[–] 0 points1 point  (1 child)

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The speed was higher than it is today, it's constantly slowed by the suns gravity.

So, it's actually higher, no?

[–] 0 points1 point  (0 children)

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I'm not sure! It's slowed by the sun's gravity but has also been accelerated by gravitational slingshotting as it headed outwards. Gravity applies its own relativistic effects. It's all very complicated. Thinking about all the factors gave me a headache, so I did the physics professor thing and ignored everything that made the concept complicated, since the key result my napkin math gives and the actual value (which would take a long time and a lot of modelling to compute) are going to boil down to about the same thing: there hasn't been much dilation. There's barely been any!

I think it's really humbling. 9.9 miles per second and it doesn't amount to anything compared to the speed of light.

[–] 1 point2 points  (0 children)

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not negligible!

[–] 85 points86 points  (62 children)

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Google provides a speed for Voyager 1 of 35,791 mi/h, which gives us approximately 0.000053 c. For the sake of argument, and because we're going to end up with a small number anyway, let's follow in the tradition of physics professors everywhere and ignore everything inconvenient. Let's pretend that it's been going that speed constantly since launch in 1977, and that the earth hasn't moved at all, and that there are no other factors involved anywhere.

The equation for time dilation factors is:

sqrt(1- v2 / c2)

v is the velocity of the moving object, and C is the speed of light. So, we get

sqrt(1 - 0.0000532 / 12 )

sqrt(0.99999999706)

So our 35 Earth years since launch have been perceived, (or would have been had its velocity been constant and nothing else moved) as 34.9999999487 years by Voyager 1.

Put another way, we've experienced 1,104,516,000 seconds, and it experienced 1,104,515,998.38 relative to our hypothetically motionless observer, or a 1.62 second difference. The actual number would be much smaller than that, since it wasn't going .000053c for the entire trip.

I think. I haven't used that equation in a long time, and will bow out for somebody who knows it better.

[–] 5 points6 points  (3 children)

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The actual number would be much smaller than that, since it wasn't going .000053c for the entire trip.

Actually, most of its journey it's been going faster than what it is now. It's constantly being slowed down by the Sun. So the difference would actually be bigger but not very much so.

Also, velocity is not the only thing affecting clocks. Being close to big masses slows down your time as well. For example, the gps satellites that are often used as an example of practical consequences of relativity. Their velocity causes the clocks of the satellites to fall behind by about 7 microseconds per day. But the effect of them being further away from Earth is actually much bigger. It causes them to get ahead 45 microseconds per day, compared to clocks on the surface. So just time dilation due to special relativity gets you an answer that's much too small and also in the wrong direction compared to what general relativity says. I haven't done the math so I'm not sure what would happen with Voyager 1 but I have a feeling that the situation may be similar.

[–] 0 points1 point  (2 children)

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Can someone figure this out, and for sake of easy calculations, as if the solar system was a point mass?

[–] 0 points1 point  (1 child)

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didnt we use Jupiter to launch it, thus we slowed its time down when it was near jupiter etc.

[–] 0 points1 point  (0 children)

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That was an extremely short period of time though.

[–] 0 points1 point  (1 child)

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I felt like using this math for the fastest man-made object, the Helios 2 solar probe. Its max speed was 0.000234c (70.22 km/s) when launched, so we'll use Jan. 15, 1976 instead of 1977.

Let's use the time dilation equation again:

v=.000234
c=1

=sqrt(1-v^2/ c^2)
=sqrt(1-.000234^2/1^2)
=sqrt(0.99999994524)

So if our time experienced from earth is 36.75 years since the launch, (or would have been had its velocity been constant and nothing else moved) Helios would return having experienced 36.7499989938 years (a difference of 0.00000100621 years).

Using seconds, Earth is 1,162,339,200 seconds, Helios is 1162339168.18, or a difference of 31.8 seconds if it traveled at that top speed constantly. A traveler on Helios 2 would be "31.8 seconds younger."

Once again, please correct me if I'm wrong with my phrasing or math.

[–]Sample Synthesis | Magnetism | Superconductivity 0 points1 point  (0 children)

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Nothing wrong with this per se, but Helios 2 is inside the orbit of Mercury, so you start having to worry about general relativity effects as well! I'm not even going to begin to try to add in that correction, though.

[–] 1 point2 points  (5 children)

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Why does c2 = 12 ?

[–] 1 point2 points  (4 children)

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In physics it's common to use units know as natural units in which various physical constants are equal to one as it can simplify the math quite a bit.

[–] 0 points1 point  (3 children)

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It just seems like c2 would be off by several orders of magnitude from 1. I guess I don't understand.

[–] 2 points3 points  (2 children)

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In natural units c=1, if you wanted to convert 1500 km/s to natural units, you'd divide 1500 km/s by the speed of light (roughly 300,000 km/s), and get a result of 0.005c. And then you can simply convert back to any other units, 0.67c is 201,000 km/s.

[–] 0 points1 point  (1 child)

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Ah. Gotcha. Thanks.

[–] 1 point2 points  (0 children)

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I could have done it in Mi/hr, but it would have just lead to huge numbers being divided by even huger numbers for an end result of a very very tiny number, which offended my sensibilities. The first thing I did was convert the units to 'c' which is the speed of light, to emphasize that it really isn't going all that fast.

[–][S] 0 points1 point  (4 children)

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Wow thanks! Yeah I haven't taken that type of physics in a long time... It is such a small thing but the thought of 1.62 seconds not existing to that object is just fascinating.

[–] 6 points7 points  (3 children)

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It did exist, for it. The difference is only perceived by a motionless observer. One with a REALLY accurate clock.

[–] 0 points1 point  (1 child)

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I would love a watch that only loses 1.6 seconds every 35 years

[–] 0 points1 point  (0 children)

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Me too. Mine loses almost a minute a week.

[–] 0 points1 point  (0 children)

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Although that's not the whole story either. The 'motionless observer' on Earth is in a free fall trajectory (orbit around the sun) and therefore experiences the maximum proper time. Voyager is the accelerated frame (not free fall), and therefore experiences less time. If you turned it around and brought it back to Earth, it's clock would be behind ours. When you consider acceleration as well, Voyager really does experience less time. The other point to note is that comparing clocks in general relativity is only really meaningful if the clocks are brought to the same place at the same time to make the comparison :)

[–] 39 points40 points  (39 children)

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All well and good, the only issue being wording toward the end. It didn't experience 1,104,515,998.38 seconds, it experienced 1,104,515,998.38 seconds relative to a motionless observer. It will have experienced the same number of seconds that we have from its perspective.

I'm sure you know that, but this is one of those rare cases where correcting wording on the internet has some purpose.

EDIT: To reply to people below me bringing up twin paradox and acceleration, facecube's post was about just velocities. I was replying to just velocities and neglected the initial acceleration. Apologies. Thanks for reminding me about that.

[–] 16 points17 points  (38 children)

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A fair point! I revised it.

[–] 0 points1 point  (0 children)

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But in essence, if you know the average speed at which Voyager has been moving away from an Earth in motion around the sun, effectively making the Earth at rest in your math, you'd have something a bit more precise. Not that it would matter much though.

[–] 1 point2 points  (36 children)

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No, it experienced that many seconds, the motionless observer on Earth experienced 1.62 seconds more. Saying it experienced so many seconds relative to a motionless observer doesn't mean anything, it's gibberish.

Also the actual number would be higher rather than smaller since it was being slowed down by the sun's gravity as it's trajectory took it out of the solar system. It would have as well have been further in a gravitational well increasing the number further. Of course taking the Earth's motion into account would then lower the number as well.

[–] 10 points11 points  (35 children)

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But who is moving? The Earth, or voyager? You could say that voyager is staying still and Earth is moving, or that Earth is staying still and voyager is moving, or that we're both moving relative to the galactic core, or any other combination.

Someone sitting on voyager would argue that Earth has experienced 1.62 seconds less than they have. This is one of the paradoxes of special relativity - each observer thinks that the other is experiencing time dilation.

[–] 1 point2 points  (31 children)

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And that's why "motionless observer" is meaningless, which is entirely his point.

Anyway... The whole symmetry breaking thing is in the acceleration.

The voyager underwent acceleration, the Earth didn't.

Therefore the voyager has the shorter time experience. It's the same thing as the twin paradox. The twin paradox isn't a paradox, it's a phenomenon, and one of the twins really does age less.

[–] 0 points1 point  (1 child)

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What is it about acceleration that causes this effect? If it wasn't for the force felt by one of the observers, neither could determine who was actually doing the acceleration. Is there something about photos hitting matter that causes this change in frames? Does gravitational acceleration also cause this, or does one of the observers have to "feel" a force rather than just experience a relative acceleration?

[–] 0 points1 point  (0 children)

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The thing about acceleration is it is symmetry breaking. The distance between the two of you increases at a rate. That is motion. It's relative.

One of you undergoes acceleration, that's not relative. There is definitively one of you that is accelerating, and one that is not.

Being in a gravitational field also causes this, as that does count as an acceleration. In special relativity, the real importance about acceleration is the way in which you squish inertial frames together when you accelerate. It creates weird effects in the time intervals which light reaches you.

[–] 0 points1 point  (28 children)

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Forgive my ignorance but couldn't you just as well say that the earth accelerated relative to voyager?

[–] 0 points1 point  (27 children)

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Only if voyager stayed where the Earth was and the Earth rotated around the sun away from it.

If you mean that acceleration is relative... No it's not.

Motion is relative. There will always be the argument of, "Are you moving, or am I moving".

Acceleration is not relative. Acceleration can be felt, and it can be observed.

If acceleration were relative, and the difference between the frame of two humans was 100Gs, which human dies? Obviously its not relative because when you experience 100Gs you die.

[–] 0 points1 point  (26 children)

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I believe the point is, that we launched it. Due to voyager starting on earth, it was at our same time frame. When we launched it we adjusted IT'S time frame, in other words, Voyager felt time dilation.

Although due to our current position, and our current speed. did we slow it down or speed it up?

[–] 0 points1 point  (25 children)

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We sped it up, because there is relative motion between us and it, and it is the one that had rockets attached to it and felt the acceleration.

[–] 1 point2 points  (0 children)

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This is a well known issue and not really a paradox. It turns out that Voyager is the one that experiences a shorter time period, because it has experienced an acceleration.

For full explanation of this, look up the falsely named "twin paradox."

[–] 13 points14 points  (1 child)

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One could say it's "Relative"

[–] 2 points3 points  (0 children)

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I never thought I'd see this phrase used correctly. My week has been made!

[–] 2 points3 points  (4 children)

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So, you basically agreed with the first cipherer with a few more significant figures. I thought you were using 35.17 years as the total earth time at first.

[–] 0 points1 point  (1 child)

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Based on how close they were posted, it's likely this comment was started before the other post had been posted.

[–] 0 points1 point  (0 children)

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Mind blown!

[–] 1 point2 points  (1 child)

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I think we were both typing at the same time. Took me a while to unlimber my memory for that equation :)

[–] 1 point2 points  (0 children)

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well, I'm impressed with you both.

[–] 7 points8 points  (6 children)

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So I sat down and worked out the calculation with semi-rough values, and if you consider Voyager I to have been in flight for 35.17 years and that it is 1.822*1010 km away, it's experienced approximately 35.1699999 years as opposed to Earth's 35.17. Not a large time dilation.

Please feel free to correct my math, I could have made an algebraic mistake somewhere.

[–] 1 point2 points  (1 child)

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I really like having both of our answers up here. I used a rough "peak" velocity, and you used a rough "average" velocity, and after 35 years the difference only comes down to about a second and a half. It's just not going that fast!

[–] 1 point2 points  (0 children)

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Indeed!

[–] 3 points4 points  (0 children)

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Moreover, how to do it:

The relativistic factor is equal to gamma, where:

gamma = 1/sqrt(1-v2/c2) This will always give a number between 1 and infinity.

Something moving fast relative to something else experiences "time dilation", and thus the trip feels shorter. If you know the time for the slower frame, you DIVIDE it by gamma (a ratio greater than 1) to get the faster (lesser) time. Similarly, if you know the time for the fast frame, you MULTIPLY it by gamma to get the time for the slower frame. All you need to know is how to calculate gamma and if the number is expected to get bigger or smaller to remember how to do this calculation.

So if it took 1 minute Earth-speed time, it would take (1 minute)/gamma minutes. Of course, c is the speed of light, and as long as your units for velocity are in the same units, you're done.

For the voyager, dividing the above distance by the above speed gives you the average velocity. Use that to compute gamma (roughly 1.0000000015293), and divide the time by it: 35.1699999. 1/sqrt(1-(16.58 km/s)2/c2)).

It's worth knowing that as you go fast compared to something, lengths "contract", and to calculate this, you use the same factor of gamma. These are the same affects, just being calculated in two different ways (and is why we call them space-time, rather than space and time; they're very linked).

[–] 3 points4 points  (2 children)

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How much difference is that in seconds or minutes?

[–] 6 points7 points  (0 children)

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text:
# Find all complex numbers satisfying the equation.

Find all complex numbers satisfying $\cos(z) = i$.

-

## 1 Answer

Hint Use the identity $\cos(z)= \frac{e^{iz}+e^{-iz}}{2}$ and then solve the resulting quadratic equation in $e^{iz}.$

-


text:
# ddG calculation

29 posts / 0 new
ddG calculation
#1

Hello!

I am trying to run ddG calculations for protein mutations but not able to locate its python script. In the rosetta manual, it is mentioned that the script could be found at

"The developmental version can be found in the Rosetta source code in source/src/python/bindings/app/membrane/compute_ddG.py"

However, compute_ddG.py is not located at this position (/bindings/app/membrane/ does not exist!!)

Could anyone suggest the reason for for this and solution as well?

Malkeet

Post Situation:
Sun, 2017-06-25 07:53
malkeet.singh

I can't find that file, nor can I find a file at that path looking through the git history.  Link me to the manual page you are looking at and we'll have a better shot at finding it.

Mon, 2017-06-26 08:54
smlewis
Tue, 2017-06-27 00:38
malkeet.singh

I'm told it is called "protocol_capture/mp_ddg/predict_ddG.py" and should be in the mp_ddg demo.

Mon, 2017-06-26 10:06
smlewis

hello !

i tried to run ddG_monomer application, and got following error. I tried to generate constraint file with "minimize_with_cst.static.linuxgccrelease" script using single PDB and a list of PDBs. but it ended up with the error

("ERROR: Unable to open weights/patch file. None of (./)standard or (./)standard.wts or /home/gnss/singhma/rosetta/software/rosetta_2017/main/database/scoring/weights/standard or /home/gnss/singhma/rosetta/software/rosetta_2017/main/database/scoring/weights/standard.wts exist")

genesis:/home/gnss/singhma/rosetta/test> /home/gnss/singhma/rosetta/software/rosetta_2017/main/source/bin/minimize_with_cst.static.linuxgccrelease -l pdblist -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /home/gnss/singhma/rosetta/software/rosetta_2017/main/database/ -ddg::harmonic_ca_tether 0.5 -score:weights standard -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false -score:patch /home/gnss/singhma/rosetta/software/rosetta_2017/main/database/scoring/weights/score12.wts_patch > mincst.log

Thanks!

Malkeet

Tue, 2017-06-27 03:31
malkeet.singh

in the protein minimizer application, the protein can be minimized with constraints.  for the demo, cst file is already given. in case, we have to do it on another protein, then how to generate the specific cst file. can anyone, suggest or share link for this?

Thanks!

Tue, 2017-06-27 04:31
malkeet.singh

Constraints documentation is here: https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/constraint-file

The sample file is all-backbone-heavy-atom coordinate constraints.  You don't actually need that for simple relax - i'm pretty sure there's a flag for it in relax already (constrain_relax_to_start_coords)

Wed, 2017-06-28 05:58
smlewis

hello!

in ddG minimization protocol:

Score12, 13 and pre_talaris_2013_standard are there. here, pre_talaris_13_std (X) score12_patch is equal to score 12. so what is teh difference between score13 and pre_talaris_13_std. they files have different values.

thanks!

Tue, 2017-06-27 05:58
malkeet.singh

score12 and pre_talaris_13 are the same thing - the latter is a backwards-compatibility mode created after we switched to Talaris.

I don't know what score13 is exactly, but it's probably something purpose built for DDG, or maybe it's related to the scorefunction development that was meant to replace score12 but became talaris13 instead.

Wed, 2017-06-28 06:00
smlewis

score13 was indeed an abandoned attempt at making a successor to score12.  It's not really related in any way to talaris2013, other than being part of the long effort to improve upon score12.

Thu, 2017-06-29 07:32
rmoretti

Hello!

Thanks to rosetta developers !!!!

I finished calculting ddG for my protein mutations and it worked fine! But I have some questions regarding the protocol.

1.  Do i need to run use 'relax protocol' prior to perform ddG calcultions because minimization is performed in ddG too (minimize_with_cst)?

2. Could I prepare the protein using 'relax protocol' and generate .cst file seperately without minimizing the protein in ddG protocol (minimize_with_cst)? because in min_with_cst (ddG protocol), my protein terminal is disturbed significantly. In relax protocol, I can control it, but not aware how to control it in min_with_cst of ddG calculation.

3. How to prepare .cst file for minimizer ?

Many thnaks!

Wed, 2017-06-28 03:48
malkeet.singh

Should you relax first?  I don't think anyone knows.  The Kellogg ddg paper from several years ago makes a determination of  whether you should or not (I don't remember the answer) - so if you are copying that protocol exactly, do what the paper says.  Otherwise, results vary depending on the setting.  Global relax tends to introduce a lot of noise, but no relax at all also introduces problems leftover from the crystal structure.

2.  I don't understand the question.  Probably yes.

3.  I've linked you to the constraint file documentation above.  I don't know where the script used to make that exact sample file is but I've asked.

Wed, 2017-06-28 06:14
smlewis

Hello!

After, having interesting time on the ddG tutorials, I shifted to real work- my protein. my protein has a ATP molelcule and a Mg ion in the PDB file.

1. In the 'relax' run, ATP was not recognized, so i ingoned it. it is not present in the output PDB as well, but i need it for further calculations. How to keep it and process in relax (without ignoring)?

2. then I used minimize_with_cst and finally the ddg_monomer......linixgccrelease: here it is ending up with in error 'caught exception atom 'CA 227' not found' which is a mg2+ ion. How to proceed for it  (i have already used a flag -ignore_unrecognized_res, but still the error persists)

Thanks!

Wed, 2017-06-28 06:41
malkeet.singh

1. You need a params file for ATP.  It's common, so one way is via https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation#setting-up-rosetta-3_obtaining-additional-files_pdb-chemical-components-dictionary.  You can also generate a parameters file yourself with molfile_to_params - look around the forums / wiki for more information.

2. I beleive the ddg_monomer application is just flatly incompatible with ligands (thus "monomer").

Wed, 2017-06-28 07:05
smlewis

Hello smlewis!

1. I tried as per you suggestion using "-in:file:load_PDB_component" flag . I downloaded CCD (chem comp dic) and copied that to /main/database/chemical, and ran the relax protocol. It worked fine and the ATP and Mg2+ are present in the relax output PDF file, but the positions of ATP and Mg2+ are highly disturbed (protein BB is OK). Could you suggest some reason for this?

2. When -in:file:load_PDB_component flag is used, how the ligands are treated? I mean, If the crystal structure conformation of ligand is taken and simply incorporated into the relax protocols' output PDB or the ligand conformation is optimized respect to protein conformations.

3.  As you told that ddg_monomer is incompatible with the ligands, so ii tried with predict_ddg.py script but i am getting this error.

genesis12:/home/gnss/singhma/rosetta/test/cftr> /home/gnss/singhma/rosetta/software/rosetta_2017/demos/public/mp_ddg/predict_ddG.py -p 2pze_relax-zn.pdb -r 75 -m P -a 10 -t true -v 7.4
Traceback (most recent call last):
File "/home/gnss/singhma/rosetta/software/rosetta_2017/demos/public/mp_ddg/predict_ddG.py", line 25, in <module>
import rosetta.protocols.membrane
ImportError: No module named rosetta.protocols.membrane

Could you please suggest me its solution? and moreover, it is possible to use protein with ATP and Mg2+ to calculate ddG using predcit_ddg script?

Thanks!

malkeet

Thu, 2017-06-29 04:32
malkeet.singh

On 1., check the tracer output of the runs - if you're getting a notice about repacking the ADP residue because of missing atoms, that might be the cause.

On 2. The -in:file:load_PDB_component option is a very minimal approach to keep non-protein residues present. The ligand should indeed be present and interacting with the rest of the protein during the protocol, but there's little treatment of the dynamic flexibility of the ligand. Instead it relies on the input coordinates to be present and preserved through the protocol. If you repack (even an implicit repacking due to missing atoms) then there's a reasonable chance you'll mess up the conformation of your ligand.

Another thing to keep in mind is that the -in:file:load_PDB_component option for ligand loading will take the version of the ligand that's in the wwPDB's chemical components dictionary. Depending on how they've represented things, this may not be what you want. For example, many of their compounds are in their uncharged form, rather than the protonation state they'd be in for neutral solution. This may be an issue with ATP, as you may end up with protonated phosphates. It may be better to manually create an ATP params file and feed that to Rosetta with -extra_res_fa instead: https://www.rosettacommons.org/demos/latest/tutorials/prepare_ligand/prepare_ligand_tutorial  This will also allow you to make a rotamer library for ATP, which will help address the packing issue.

3. Do you have PyRosetta installed? The predict_ddG.py script is a PyRosetta script, and thus requires a working installation of PyRosetta. If you just have the commandline version of Rosetta, it won't work.

The other caveat is that predict_ddG.py  is intended for membrane proteins. If you have a soluble protein, it might not work out well.

Thu, 2017-06-29 07:46
rmoretti

The ATP conformation problem seems to be due to repacking as -in:file:load_PDB_component option is taking the information from wwPDB's chemical components dictionary. so thePARAM file might overcome this problem. I will try it.

the ultimate question is: I have to analyze the ddG change in protein mutants, and my protein has Mg2+ and is non-transmembrane too. So what should i do to handle it, as predict_ddg.py script tackle membrane proteins and monomer_ddg can't handle ligands (Mg2+). Is there any way to proceed with the work using Rosetta ddG applications?

Thanks!

Thu, 2017-06-29 10:09
malkeet.singh

There's various ddG of folding scripts for RosettaScripts running around, which can probably be re-purposed for your needs. The group who has put in the most effort into these protocols recently is probably the Kortemme lab at UCSF. I'm not sure if they've published anything on their work yet, though. Their most recent publication in the area that I can find (https://doi.org/10.1371/journal.pone.0130433) apparently still uses the ddg_monomer application (see https://guybrush.ucsf.edu/benchmarks/benchmarks/DDG)

That said, I belive the ddg_monomer application has had some bug fixes in it to allow non-protein residues. If you're not using a very recent weekly release, you may want to try updating your Rosetta version and see if that fixes things.

Thu, 2017-06-29 13:15
rmoretti

Hello!

I ran the relax protocol with following parameters, with which it was successful but ligand was not incorporated in the final PDB.

for metal, I used : -in:auto:setup_metals >> metal incorporated in the final version of PDB.

param file of the crystal ligand used with : -extra:res_fa 'path to param file' >> no ligand in the final PDB.

Could you pls suggest how to tackle the crystal ligand in relax protocol?

in other PDB (metal and ligand), the error is displayed: segmentation fault (core dumped)>> what is this??

malkeet

Thu, 2017-07-06 07:12
malkeet.singh

For the first question:

Do we know that it read and tried to use your parameter file?  Did you leave the chemical components dictionary active, or did you turn that flag off?  I suspect Rocco wrote it such that it will use a user-passed parameter file over an automatic parameter set from the chemical components dictionary - but if they aren't lined up perfectly, it will use the wrong one and you won't notice the problem.  So, check these things:

1) make sure that the params file and the PDB are using the exact same 3-letter code for the ligand

2) make sure that -ignore_unrecognized_res and the flags for the chemical components dictionary are OFF

For the second queston: If you google segmentation fault, you'll see that it is a highly generic error that just means that illegal memory was accessed.  We can't tell you what the problem was just from the fact that it segfaulted.  The standard advice is A) look at the log file to see if there is something useful nearby, B) recompile and rerun in debug mode, which will sometimes produce more useful errors (at the cost of being slower).  (the  extra checks debug mode does are what makes it slow, but it also makes the errors clear instead of just crashing).

Thu, 2017-07-06 08:08
smlewis

Hello!

In the relax protocol, if run without constraints, the repacking of side chains significantly change the final structure. Is there some specific reason for repacking the side chains instead of simple minimization?

Any paper explaining the basics of this protocol?

Mon, 2017-07-10 06:46
malkeet.singh

One way to look at this is "how fixed are those sidechains in reality"?  For most structures, only the core sidechains have sufficient density to unambiguously assign rotamers, and even then they'll move as the protein 'breathes'.

The point of relax is to take a structure and modify it to fit Rosetta's scorefunction.  It can acheive much lower scores by repacking the sidechains - both by editing out lots of sidechain-involved clashes, and by refitting rotamers into rotamer wells.  The rotamericity of crystal structures is sometimes pretty poor (or at least without sufficient evidence to go off-rotamer).  If the point of relax is to find lower-energy structures, repacking is better because if finds lower-energy structures.  If you are relaxing for some other reason, it might not be best.

Relaxing with strong constraints is better when either A) you know the crystal is right and the change Rosetta wants to make is wrong, or B) you just want to improve the worst parts of the structure without giving Rosetta free rein.

There are no papers on relax diretly.  Relax was created as the back half of ab-initio: it lets you start with a centroid model from ab initio structure prediction and turn it into a fully atomic model.  This HAS to repack, because there was no sidechain data in the starting model.  I assume some of the older (but not oldEST) papers on structure prediction describe relax.

Mon, 2017-07-10 10:49
smlewis

Hello!!

In the relax protocol, I used another PDB which don’t have any metal ion (2RNU). I deleted the sulfate ion and use chain A of this protein that contained a protein, waters and crystal ligand.

For relax, I used –relax:consrain_relax_to_start_coords and crystalligand.param file of crystal ligand (CL) in two manners: only crystal conformation and a pool of generated conformers.

When I input pool of CL conformers with flag –extra_res_fa (.param file)>>CL is dispositioned badly in the final output PDB.

In case, I used a CL’s crystal conformation>> the output ligand is weird: the molecule is broken into pieces (bonds are broken).

PS: in case the PDB has only protein (no ligand)> the whole procedure is successful (I tried it on tutorial PDB 1ubq.pdb)!

Clean PDB with ligand: I copied this script into my working directory and then passed chmod +x command to make it executable. When I ran it for my PDB, following error appeared

genesis:/home/gnss/singhma/rosetta/test/> python clean_pdb_keep_ligand.py 2nru.pdb

Traceback (most recent call last):

File "clean_pdb_keep_ligand.py", line 19, in <module>

from amino acids import longer names

ImportError: No module named amino acids

Malkeet

Tue, 2017-07-11 05:44
malkeet.singh

Assuming source/src/apps/public/relax_w_allatom_cst/clean_pdb_keep_ligand.py is the one you are using - it works for me, locally.  I have a vague memory of trying to use it and having an issue, but I don't remember how it was resolved.  It was either adding something to the $PATH or$PYTHONPATH, or maybe finding the module it wanted to import from somewhere else in Rosetta's hierarchy (probably in tools) and copying/symlinking it to the directory I wanted to run in.  Rosetta/tools/python_pdb_structure/amino_acids.py is probably the file it is looking for.

If you only want to do it a few times, it's just as simple to run a functioning clean_pdb and then copy the ligand back in with a text editor.

> When I input pool of CL conformers with flag –extra_res_fa (.param file)>>CL is dispositioned badly in the final output PDB.

Rosetta is presumably telling you that it doesn't like where the ligand is, for whatever reason.  You'll have to use your own knowledge of the system to determine if Rosetta is wrong or if the system is wrong.  Constraints are the way to override Rosetta.

> In case, I used a CL’s crystal conformation>> the output ligand is weird: the molecule is broken into pieces (bonds are broken).

How large is the molecule?  It's not split up into multple params files?  Are you using cartesian minimization in your relax?  My best guess is that the cartesian step, if present, doesn't understand the molecule (lack of parameters for it; the tools that generate ligand params can't do so for cartesian minimization) and is letting the bonds it doesn't know about break.

Tue, 2017-07-11 07:45
smlewis

Hello Rosetta Developers!

In continuation to my previous discussion on this forum, I completed ddg calculations for ~40 protein mutations without considering ligand and metal ion. I got good results. Now, I am looking forward to calculate ddg values considering ligand (ATP) and metal ion into the active site (mg), which is supposed to further improve the results.

1. first I need to relax the protein-crystal ligand (CL) complex: here if i use CL without constraints, the CL in the final PDB is totally disturbed. I tried to understand 'cstfile' provided in the tutorial of the minimizer. But I could not get it exactly. I have to impose restraint on the ATP molecule for which I have coordinates available. Could you please explain a bit how to proceed for this.

2. In relax protocol, there are parameters for Mg2+ so can I use them (or anyhow by doing some changes) to include and score in ddg_monomer run (ddg calculation)?

3. Similarly, is there any way to include (with restrains) ATP into ddg calcaultions?

Many Thanks!

Malkeet

Wed, 2017-08-23 09:38
malkeet.singh

See the constraint file documentation for more information on putting together a constraint file. You should be able to use that during the relax/minimization phases.

I'd probably recommend against coordinate constraints, and look more toward atom pair (distance) constraints. That is, you pick pairs of atoms which should stay about the same distance apart, and impose a constraint between them. I'd suggest an iterative approach, where you do the relax/minimization, look at what moved but shouldn't, add constraints to those pairs, rerun the relax/minimization, and then iterate the process until you get what you want.

Adding ATP to the run should theoretically be as simple as adding the appropriate params file for ATP. However, I know that various versions of the ddG protocol have historically had issues with non-protein residues, so there may be bugs you'll need to work around/through.

Wed, 2017-08-23 11:45
rmoretti

Hello!

bingo! My monomer_ddg worked for metal and ligand. Below, I shall mention the hassles.

- The first step in the ddg_monomer (ddg calculation) is the protein minimization with constraints using minimize_with_cst.static.linuxgccrelease. In this step protein, metal and ligand combination works well and generate a xxx.cst file (constraints file).

- thereafter the ultimate step is ddg calclulation using ddg_monomer.static.linuxgccrelease where metal and ligand are not recognized and run failed.

- the reason is, minimize_with_cst.static.linuxgccrelease script generates xxx.cst file in which the constraint is generated on CA atoms and if you open the file and observe, metal and ligand atoms are also marked as CAs which indeed are not. So changing the notation of these atoms to correct one solved the problem. For instance, I have Mg ion in my protein so I changed CA marked at mg position to MG and it worked.

Dear Rosetta developers!

Thanks for bearing with me and replying timely to my questions.

Best of luck!

malkeet

Tue, 2017-08-29 01:38
malkeet.singh

Hello!

My ddg calclulations using ref2015 is taking about >1 day/mutation running on 2.8 GHz processor. Is it likely to happen ?or there is something fishy since this was not the case if I use talaris on same CPU.

Thanks!

Malkeet

Tue, 2017-08-29 04:46
malkeet.singh

Hello!

Prior to use my protein for dg calculations, I want to use relax and also don't want metal and ATP to move inappropriately.  As per your suggestions, I tried constraints.

-atompair: In this,  I used all N and P of ATP and CA of two residues (~16 lines or constraints). for Mg, I used 4 constraints with CA of 4 amino acids. I used the constraint values starting from 0.5 to 50 even, my ATP and Mg are disturbed in the final structure. I didn't get why? I am using ATP.param file in which there is one structure (obtained from crystal structure) because I don't want different conformation of ATP. ()

-coordinate constraint: in this,  I used the X,Y,Z coordinates of ATP and Mg and CA of one amino acid as a reference to set constraint. Here also the Mg and ATP in the final structure are totally disturbed. Moreover, in the sample cstfile, after Harmonic two numbers are given. could you tell me the significance of both (e.g. 0.2  0.1).

these are general flags that I used

-run:min_type lbfgs_armijo_nonmonotone
-run:min_tolerance 0.001
-constraints:cst_file cstfile
-score:weights ref2015_cst
-out:suffix _minwithcsts
-relax:constrain_relax_to_start_coords
-out:level 400
-relax:default_repeats 1
-ignore_waters
-use_input_sc
-nstruct 1

-extra_res /path/ATP.params

kindly suggest me solution for these hassles.


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# mean squre error Congerville, Illinois

All rights reserved. Note that I used an online calculator to get the regression line; where the mean squared error really comes in handy is if you were finding an equation for the regression However, one can use other estimators for σ 2 {\displaystyle \sigma ^{2}} which are proportional to S n − 1 2 {\displaystyle S_{n-1}^{2}} , and an appropriate choice can always give Required fields are marked *Comment Name * Email * Website Find an article Search Feel like "cheating" at Statistics?

For example, in a linear regression model where is a new observation and is the regression estimator       with variance , the mean squared prediction error for is   Mean squared error From Wikipedia, the free encyclopedia Jump to: navigation, search "Mean squared deviation" redirects here. Since an MSE is an expectation, it is not technically a random variable. If the estimator is derived from a sample statistic and is used to estimate some population statistic, then the expectation is with respect to the sampling distribution of the sample statistic.

It would have the same effect of making all of the values positive as the absolute value. 2. The root-mean-square deviation (RMSD) or root-mean-square error (RMSE) is a frequently used measure of the differences between values (sample and population values) predicted by a model or an estimator and the That is, the n units are selected one at a time, and previously selected units are still eligible for selection for all n draws. Thus, the best measure of the center, relative to this measure of error, is the value of t that minimizes MSE. 1.

Find a Critical Value 7. Barry Van Veen 28.900 προβολές 12:30 Φόρτωση περισσότερων προτάσεων… Εμφάνιση περισσότερων Φόρτωση... Σε λειτουργία... Γλώσσα: Ελληνικά Τοποθεσία περιεχομένου: Ελλάδα Λειτουργία περιορισμένης πρόσβασης: Ανενεργή Ιστορικό Βοήθεια Φόρτωση... Φόρτωση... Φόρτωση... Σχετικά με Τύπος Carl Friedrich Gauss, who introduced the use of mean squared error, was aware of its arbitrariness and was in agreement with objections to it on these grounds.[1] The mathematical benefits of This also is a known, computed quantity, and it varies by sample and by out-of-sample test space.

There are, however, some scenarios where mean squared error can serve as a good approximation to a loss function occurring naturally in an application.[6] Like variance, mean squared error has the Forgot your Username / Password? How to Calculate a Z Score 4. Probability and Statistics (2nd ed.).

Tech Info LibraryWhat are Mean Squared Error and Root Mean SquaredError?About this FAQCreated Oct 15, 2001Updated Oct 18, 2011Article #1014Search FAQsProduct Support FAQsThe Mean Squared Error (MSE) is a measure of MSE is a risk function, corresponding to the expected value of the squared error loss or quadratic loss. If the statistic and the target have the same expectation, , then       In many instances the target is a new observation that was not part of the analysis. Sign Up Thank you for viewing the Vernier website.

You can change this preference below. Κλείσιμο Ναι, θέλω να τη κρατήσω Αναίρεση Κλείσιμο Αυτό το βίντεο δεν είναι διαθέσιμο. Ουρά παρακολούθησηςΟυράΟυρά παρακολούθησηςΟυρά Κατάργηση όλωνΑποσύνδεση Φόρτωση... Ουρά παρακολούθησης Ουρά __count__/__total__ Overview Mean Squared Error: Definition and Example was last modified: February 15th, 2016 by Andale By Andale | November 2, 2013 | Statistics How To | No Comments | ← Degrees of T Score vs. Insert your X values into the linear regression equation to find the new Y values (Y').

References ^ a b Lehmann, E. The denominator is the sample size reduced by the number of model parameters estimated from the same data, (n-p) for p regressors or (n-p-1) if an intercept is used.[3] For more For an unbiased estimator, the MSE is the variance of the estimator. The denominator is the sample size reduced by the number of model parameters estimated from the same data, (n-p) for p regressors or (n-p-1) if an intercept is used.[3] For more

In statistical modelling the MSE, representing the difference between the actual observations and the observation values predicted by the model, is used to determine the extent to which the model fits The goal of experimental design is to construct experiments in such a way that when the observations are analyzed, the MSE is close to zero relative to the magnitude of at The two components can be associated with an estimator’s precision (small variance) and its accuracy (small bias). The class mark of the i'th class is denoted xi; the frequency of the i'th class is denoted fi and the relative frequency of th i'th class is denoted pi =

For example, the above data is scattered wildly around the regression line, so 6.08 is as good as it gets (and is in fact, the line of best fit). The two should be similar for a reasonable fit. **using the number of points - 2 rather than just the number of points is required to account for the fact that The smaller the means squared error, the closer you are to finding the line of best fit. Addison-Wesley. ^ Berger, James O. (1985). "2.4.2 Certain Standard Loss Functions".

It is just the square root of the mean square error. Analytics University 1.372 προβολές 8:10 (ML 11.1) Estimators - Διάρκεια: 12:33. This property, undesirable in many applications, has led researchers to use alternatives such as the mean absolute error, or those based on the median. Scott Armstrong & Fred Collopy (1992). "Error Measures For Generalizing About Forecasting Methods: Empirical Comparisons" (PDF).

Descriptive Statistics Υπενθύμιση αργότερα Έλεγχος Υπενθύμιση απορρήτου από το YouTube, εταιρεία της Google Παράβλεψη περιήγησης GRΜεταφόρτωσηΣύνδεσηΑναζήτηση Φόρτωση... Επιλέξτε τη γλώσσα σας. Κλείσιμο Μάθετε περισσότερα View this message in English Το Khan Academy 500.685 προβολές 15:15 Least squares | MIT 18.02SC Multivariable Calculus, Fall 2010 - Διάρκεια: 9:05. In computational neuroscience, the RMSD is used to assess how well a system learns a given model.[6] In Protein nuclear magnetic resonance spectroscopy, the RMSD is used as a measure to Values of MSE may be used for comparative purposes.

Wikipedia® is a registered trademark of the Wikimedia Foundation, Inc., a non-profit organization. Retrieved from "https://en.wikipedia.org/w/index.php?title=Mean_squared_error&oldid=741744824" Categories: Estimation theoryPoint estimation performanceStatistical deviation and dispersionLoss functionsLeast squares Navigation menu Personal tools Not logged inTalkContributionsCreate accountLog in Namespaces Article Talk Variants Views Read Edit View history Statisticshowto.com Apply for $2000 in Scholarship Money As part of our commitment to education, we're giving away$2000 in scholarships to StatisticsHowTo.com visitors. Depending on your data, it may be impossible to get a very small value for the mean squared error.