Re: [ccp4bb] rmsd calculation. .

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Subject: rmsd calculation
From: Jenny ruisher {- at -} GMAIL {- dot -} COM
Date: 2007-05-10

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Subject: Re: rmsd calculation. .
From: "Kerr, Iain" Iain {- dot -} Kerr {- at -} STJUDE {- dot -} ORG
Date: 2007-05-10

Hi Jenny,

You can do this in LSQMAN (if I'm understanding your question
correctly...)

You'd first superimpose the residues in the "fixed region" to give a
superimposed core using the 'EXplicit' command, eg:

LSQMAN > ex m1
Range 1 ? (A1-10) "a4-10 a19-23 a28-36 a44-51 a53-66 a91-97 a106-111
a123:126"
Mol 2 ? (M1) m2
Range 2 ? (A1) "a4 a19 a28 a44 a53 a91 a106 a123"
Explicit fit of M1 "A4-10 A19-23 A28-36 A44-51 A53-66 A91-97 A106-111
A123:126"
And M2 "A4 A19 A28 A44 A53 A91 A106 A123"
Atom types
CA
N
C
O
CB

Nr of atoms to match : ( 295)
The 295 atoms have an RMS distance of 0.892 A
Rotation : -0.956932 0.127723 -0.260706
0.170532 -0.479456 -0.860837
-0.234946 -0.868222 0.437026
Translation : 13.787 26.800 38.541

Then use the "IMProve" command to iteratively improve the fit over all
CAs...this only works for two molecules at a time though...I guess
choose a fixed standard to align all the others against. Remember to
write out the coordinates for the rotated (ie. "m2") molecules:

* apply m1 m2

* wr m2 blah_rotated.pdb

Then to calculate the RMSDs for just the loop regions compare the
superimposed molecules to the fixed standard (ie. "m1" is the fixed
standard, "m2" is your blah_rotated.pdb), explicitly using just the loop
atoms this time in "m1" and "m2" ranges.

I'm sure there is an easier way to do this, but works for me.

HTH,

Iain

________________________________

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Jenny
Sent: Thursday, May 10, 2007 5:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] rmsd calculation. .

Hi, All,

I have a question about rmsd calculation.

I have some pdbs (100 residues ) and these pdbs differ pretty much only
the loop region 40-60. Is there any easy way that I can superimpose the
fixed region ( 1-40,60-100) and then calculate the rmsd for the loop?I
need to calculate for each pair, so if there is any script or program
available to do this quickly, that would be great.

Thanks.

Jenny

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CCP4bb <-- 2007 <-- May 2007 <-- 10 May 2007

Previous message:
Subject: rmsd calculation
From: Jenny ruisher {- at -} GMAIL {- dot -} COM
Date: 2007-05-10

Next message:
Subject: Molecular Replacement issues with a WD-40 7-bladed beta propeller
From: Scott Coyle scoyle79 {- at -} BERKELEY {- dot -} EDU
Date: 2007-05-10