Re: [ccp4bb] Help with Superpose results
You are quite right - LSQKAB must be wrong to report a RMS Distance?/deviation? for a GLY side chain - will look into it and correct I hope.. Thanks for noticing it and pointing the bug out Eleanor Nathalie Colloc'h wrote: Hello all, I have still a question about LSQKAB Why LSQKAB gives a rmsd (or a rms xyz I don't mind) non null for glycine side chains ? thanks a lot nathalie Eleanor Dodson a écrit : Q1) Rms xyz and rmsd mean exactly the same . And as for what you should report - that depends on the problem. As long as you state clearly what has been fitted ( all atoms, CAs, loops excluded etc etc ) Q2) The algorithms for SSM and LSQKAB are different - SSM fits secondary structure elements only, then checks the rmsd of all CAs. This is particularly useful for fitting homolous proteins. LSQKAB requires a list of all the atoms to be matched and that rms xyz considers all those atoms and only those. If you want a report of all differences you must click for that on the GUI. And as you say this is helpful for finding differences in different copies of the same molecule. Eleanor
Re: [ccp4bb] Help with Superpose results
You originally referred to statistics, and from statistical point of
view different structures have different underlying probability
distributions. In statistics the rms DEVIATION (or standard deviation)
refers to the variation of a random variable. With rms DISTANCE between
two structures you are not looking at a random variable, you are looking
at the ensemble of random variables (each being the distance between two
homologous atoms). So from STATISTICAL point of view, it is not an
example of rms deviation. These are semantics, of course, but I hope
this is the clarification you asked for.
You're welcome anyway...
Ed.
1. On Tue, 2008-04-08 at 21:33 +0200, Philippe DUMAS wrote:
Apparently I had missed some subtle considerations...
Yet, I confess am not fully convinced: is it so wrong to speak of how much
different structures DEVIATE from each other ? I do not see what prevents
you from defining the correct underlying probability distribution. That
interatomic distances can be used to quantify deviations does not hurt me so
much.
Thank you anyway...
Philippe Dumas
IBMC-CNRS, UPR9002
15, rue René Descartes 67084 Strasbourg cedex
tel: +33 (0)3 88 41 70 02
[EMAIL PROTECTED]
-Message d'origine-
De : Ed Pozharski [mailto:[EMAIL PROTECTED]
Envoyé : Tuesday, April 08, 2008 3:56 PM
À : Philippe DUMAS
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
RMS deviation refers to the variance of a random variable - it is a
characteristic of the underlying probability distribution. When you
superpose two different structures, you are looking at the DISTANCE
between atoms, not the DEVIATION in their position. In fact, for
individual atoms you can't even say root-mean-square, it's just plain
distance. The core argument is that you are looking at two structures
that represent different underlying probability distributions, and so
it's definitely not the rms deviation you are calculating, but rms
distance (rms over all the atoms in the structure). HTH,
Ed.
On Tue, 2008-04-08 at 11:07 +0200, Philippe DUMAS wrote:
Although this is not a very important issue..., I am a bit surprised by
Gerard's insistance for a 'stop calling rmsd rms deviation'. Isn'it a
general term in statistical studies, valid for distances separating
homologous atoms as well as for any other factor (B factors for example) ?
Philippe Dumas
IBMC-CNRS, UPR9002
15, rue Rene Descartes 67084 Strasbourg cedex
tel: +33 (0)3 88 41 70 02
[EMAIL PROTECTED]
-Message d'origine-
De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de
Gerard DVD Kleywegt
Envoye : Monday, April 07, 2008 7:20 PM
A : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
Is the rms xyz displacement equivalent to an rmsd??
yes. it is in fact a better name than rms deviation, although i think
'root-mean-square distance' is even better, as it says exactly what you
calculate.
think of it like this, the formula for rmsd is:
RMSD = square-root [ SUM(atoms) { (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 } /
Natoms
]
now, (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 is the Square of the Distance
between
two equivalenced atoms in structure 1 and 2; adding them for all pairs of
equivalenced atoms and dividing by the number of atoms gives you the Mean
Squared Distance; finally, taking the square root yields the
Root-Mean-Square
Distance, or RMSD
so, people, can we all please stop calling rmsd rms deviation - it
really
is
an rms distance (or rms displacement). you could argue that the
formula
gives some kind of rms coordinate deviation, but in that case you ought to
divide by 3*Natoms instead.
(having said that, the term RMS B displacement sounds positively silly!)
--dvd
**
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
**
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
**
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /
--
Edwin Pozharski, PhD, Assistant
Re: [ccp4bb] Help with Superpose results
A horrible bug - this line was somehow lost from lsqkab in the mists of time: Lines 1029-132 - ish should be IF (ATNMW(I)(1:3).EQ.'CA ' .OR. ATNMW(I)(1:3).EQ.'N ' .OR. + ATNMW(I)(1:3).EQ.'C ' .OR. ATNMW(I)(1:3).EQ.'O ' .OR. + ATNMW(I)(1:3).EQ.'P ' .OR. ATNMW(I)(1:3).EQ.'O1P' .OR. etc NOT IF (ATNMW(I)(1:3).EQ.'CA ' .OR. ATNMW(I)(1:3).EQ.'N ' .OR. + ATNMW(I)(1:3).EQ.'P ' .OR. ATNMW(I)(1:3).EQ.'O1P' .OR. Thank you for noticing this! Eleanor Nathalie Colloc'h wrote: Hello all, I have still a question about LSQKAB Why LSQKAB gives a rmsd (or a rms xyz I don't mind) non null for glycine side chains ? thanks a lot nathalie Eleanor Dodson a écrit : Q1) Rms xyz and rmsd mean exactly the same . And as for what you should report - that depends on the problem. As long as you state clearly what has been fitted ( all atoms, CAs, loops excluded etc etc ) Q2) The algorithms for SSM and LSQKAB are different - SSM fits secondary structure elements only, then checks the rmsd of all CAs. This is particularly useful for fitting homolous proteins. LSQKAB requires a list of all the atoms to be matched and that rms xyz considers all those atoms and only those. If you want a report of all differences you must click for that on the GUI. And as you say this is helpful for finding differences in different copies of the same molecule. Eleanor
Re: [ccp4bb] Help with Superpose results
Hello all, I have still a question about LSQKAB Why LSQKAB gives a rmsd (or a rms xyz I don't mind) non null for glycine side chains ? Disclaimer: The following is just humor with the best intentions to entertain the bb audience and not aiming to annoy anybody, but hoping that some people might indeed think twice before they post a question. If you get usually annoyed by my jokes (... or Gerard's ...) do not read any further. No minorities are hurt by the joke though, unless there is really a crystallographer called Percy. Now, read the attached text and instead of Infanta's eyes think of glycine side chain in my structure, instead of Stone of Galveston read glycine side chain in the reference structure and more beautiful/blue in our case more similar. regards to everybody A. PS Thanks to Richard Curtis for the original text ;-) Percy: You know, they do say that the Infanta's eyes are more beautiful than the famous Stone of Galveston. Edmund: Mm! ... What? Percy: The famous Stone of Galveston, My Lord. Edmund: And what's that, exactly? Percy: Well, it's a famous blue stone, and it comes ... from Galveston. Edmund: I see. And what about it? Percy: Well, My Lord, the Infanta's eyes are bluer than it, for a start. Edmund: I see. And have you ever seen this stone? Percy: (nods) No, not as such, My Lord, but I know a couple of people who have, and they say it's very very blue indeed. Edmund: And have these people seen the Infanta's eyes? Percy: No, I shouldn't think so, My Lord. Edmund: And neither have you, presumably. Percy: No, My Lord. Edmund: So, what you're telling me, Percy, is that something you have never seen is slightly less blue than something else you have never seen. Percy: (finally begins to grasp) Yes, My Lord.
Re: [ccp4bb] Help with Superpose results
Although this is not a very important issue..., I am a bit surprised by
Gerard's insistance for a 'stop calling rmsd rms deviation'. Isn'it a
general term in statistical studies, valid for distances separating
homologous atoms as well as for any other factor (B factors for example) ?
Philippe Dumas
IBMC-CNRS, UPR9002
15, rue Rene Descartes 67084 Strasbourg cedex
tel: +33 (0)3 88 41 70 02
[EMAIL PROTECTED]
-Message d'origine-
De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de
Gerard DVD Kleywegt
Envoye : Monday, April 07, 2008 7:20 PM
A : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
Is the rms xyz displacement equivalent to an rmsd??
yes. it is in fact a better name than rms deviation, although i think
'root-mean-square distance' is even better, as it says exactly what you
calculate.
think of it like this, the formula for rmsd is:
RMSD = square-root [ SUM(atoms) { (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 } /
Natoms
]
now, (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 is the Square of the Distance
between
two equivalenced atoms in structure 1 and 2; adding them for all pairs of
equivalenced atoms and dividing by the number of atoms gives you the Mean
Squared Distance; finally, taking the square root yields the
Root-Mean-Square
Distance, or RMSD
so, people, can we all please stop calling rmsd rms deviation - it really
is
an rms distance (or rms displacement). you could argue that the formula
gives some kind of rms coordinate deviation, but in that case you ought to
divide by 3*Natoms instead.
(having said that, the term RMS B displacement sounds positively silly!)
--dvd
**
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
**
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
**
Re: [ccp4bb] Help with Superpose results
Hello all, I have still a question about LSQKAB Why LSQKAB gives a rmsd (or a rms xyz I don't mind) non null for glycine side chains ? thanks a lot nathalie Eleanor Dodson a écrit : Q1) Rms xyz and rmsd mean exactly the same . And as for what you should report - that depends on the problem. As long as you state clearly what has been fitted ( all atoms, CAs, loops excluded etc etc ) Q2) The algorithms for SSM and LSQKAB are different - SSM fits secondary structure elements only, then checks the rmsd of all CAs. This is particularly useful for fitting homolous proteins. LSQKAB requires a list of all the atoms to be matched and that rms xyz considers all those atoms and only those. If you want a report of all differences you must click for that on the GUI. And as you say this is helpful for finding differences in different copies of the same molecule. Eleanor -- Dr. Nathalie Colloc'h, PhD CI-NAPS, UMR 6232 - UCBN - CNRS GIP Cyceron Bd Becquerel, BP5229 14074 Caen cedex FRANCE Tel. 33.2.31.47.01.32 Fax. 33.2.31.47.02.22 [EMAIL PROTECTED]
Re: [ccp4bb] Help with Superpose results
Sorry for this 'joke-like' question which was not intend to be a joke There was a misunderstanding about my question It is not null or not null which worry me, but it is the fact there is a value for glycine 'side chains that I know for sure having no side chains. From my point of view, it must be written n.d. (not determined) or someting like that instead of a value which differ from a gly side chain to a gly side chain (sorry for this non-sense gly side chain) best regards nathalie -- Dr. Nathalie Colloc'h, PhD CI-NAPS, UMR 6232 - UCBN - CNRS GIP Cyceron Bd Becquerel, BP5229 14074 Caen cedex FRANCE Tel. 33.2.31.47.01.32 Fax. 33.2.31.47.02.22 [EMAIL PROTECTED]
Re: [ccp4bb] Help with Superpose results
an interesting way to compare structures from the same protein sequence is reported here : acta cryst D56 714-721, 2000 objective comparison of protein structures : error-scaled difference distance matrice acta cryst D60 2269-2275, 2004 domain identification by iterative analysis of error-scaled difference distance matrices both are by T. Schneider, might find a couple others out there HTH -bryan
Re: [ccp4bb] Help with Superpose results
Apparently I had missed some subtle considerations...
Yet, I confess am not fully convinced: is it so wrong to speak of how much
different structures DEVIATE from each other ? I do not see what prevents
you from defining the correct underlying probability distribution. That
interatomic distances can be used to quantify deviations does not hurt me so
much.
Thank you anyway...
Philippe Dumas
IBMC-CNRS, UPR9002
15, rue René Descartes 67084 Strasbourg cedex
tel: +33 (0)3 88 41 70 02
[EMAIL PROTECTED]
-Message d'origine-
De : Ed Pozharski [mailto:[EMAIL PROTECTED]
Envoyé : Tuesday, April 08, 2008 3:56 PM
À : Philippe DUMAS
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
RMS deviation refers to the variance of a random variable - it is a
characteristic of the underlying probability distribution. When you
superpose two different structures, you are looking at the DISTANCE
between atoms, not the DEVIATION in their position. In fact, for
individual atoms you can't even say root-mean-square, it's just plain
distance. The core argument is that you are looking at two structures
that represent different underlying probability distributions, and so
it's definitely not the rms deviation you are calculating, but rms
distance (rms over all the atoms in the structure). HTH,
Ed.
On Tue, 2008-04-08 at 11:07 +0200, Philippe DUMAS wrote:
Although this is not a very important issue..., I am a bit surprised by
Gerard's insistance for a 'stop calling rmsd rms deviation'. Isn'it a
general term in statistical studies, valid for distances separating
homologous atoms as well as for any other factor (B factors for example) ?
Philippe Dumas
IBMC-CNRS, UPR9002
15, rue Rene Descartes 67084 Strasbourg cedex
tel: +33 (0)3 88 41 70 02
[EMAIL PROTECTED]
-Message d'origine-
De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de
Gerard DVD Kleywegt
Envoye : Monday, April 07, 2008 7:20 PM
A : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
Is the rms xyz displacement equivalent to an rmsd??
yes. it is in fact a better name than rms deviation, although i think
'root-mean-square distance' is even better, as it says exactly what you
calculate.
think of it like this, the formula for rmsd is:
RMSD = square-root [ SUM(atoms) { (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 } /
Natoms
]
now, (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 is the Square of the Distance
between
two equivalenced atoms in structure 1 and 2; adding them for all pairs of
equivalenced atoms and dividing by the number of atoms gives you the Mean
Squared Distance; finally, taking the square root yields the
Root-Mean-Square
Distance, or RMSD
so, people, can we all please stop calling rmsd rms deviation - it
really
is
an rms distance (or rms displacement). you could argue that the
formula
gives some kind of rms coordinate deviation, but in that case you ought to
divide by 3*Natoms instead.
(having said that, the term RMS B displacement sounds positively silly!)
--dvd
**
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
**
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
**
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /
