Re: [ccp4bb] Program to find the center of mass

- Protein crystallography

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Program to find the center of mass
From: Nian Huang huangnian {- at -} GMAIL {- dot -} COM
Date: 2007-05-09

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Subject: Re: Program to find the center of mass
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-05-09

Subject: Re: Program to find the center of mass
From: Tim Grune tim {- dot -} grune {- at -} SYNCHROTRON {- dot -} VIC {- dot -} GOV {- dot -} AU
Date: 2007-05-09

Hello,

Assuming that the centre of mass is close to the centre of geometry for a
protein, you could use
grep -e "^ATOM
^HETATM" 1AQB.pdb
cut -b 31-54

awk '{ x+=$1; y+=$2; z+=$3; } END
{print "Centre of mass: (" x/FNR "y/FNR " z/FNR"}'

or you could use G. Kleywegt's 'moleman2' and use the 'stat' command.
Tim

On Thursday 10 May 2007 09:43, Nian Huang wrote:
> Dear all,
>
> I was trying to do a NCS averaging of the map using Resolve. I had a
> partial model, which generated a rotation and translation matrix by
> program lsqkab. Resolve also requires a center of mass input. Do you
> know any program can estimate it either by map or pdb file?
> Thanks.
>
> Nian Huang
> Department of Biochemistry
> Univ of Texas Southwestern Medical Center

--
Tim Grune
Australian Synchrotron
800 Blackburn Road
Clayton, VIC 3168
Australia

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Program to find the center of mass
From: Nian Huang huangnian {- at -} GMAIL {- dot -} COM
Date: 2007-05-09

Next message:
Subject: Re: Program to find the center of mass
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-05-09