Re: [ccp4bb] Help with Superpose results

2008-04-09 Thread Eleanor Dodson
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

Re: [ccp4bb] Help with Superpose results

2008-04-09 Thread Ed Pozharski
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

Re: [ccp4bb] Help with Superpose results

2008-04-09 Thread Eleanor Dodson
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 '

Re: [ccp4bb] Help with Superpose results

2008-04-08 Thread Anastassis Perrakis
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

Re: [ccp4bb] Help with Superpose results

2008-04-08 Thread Philippe DUMAS
: 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

Re: [ccp4bb] Help with Superpose results

2008-04-08 Thread Nathalie Colloc'h
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

Re: [ccp4bb] Help with Superpose results

2008-04-08 Thread Nathalie Colloc'h
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

Re: [ccp4bb] Help with Superpose results

2008-04-08 Thread Bryan W. Lepore
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

Re: [ccp4bb] Help with Superpose results

2008-04-08 Thread Philippe DUMAS
, 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