Re: [ccp4bb] RMSD of pairs of atoms?

- Protein crystallography

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

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From: pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-03-01

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Subject: Re: RMSD of pairs of atoms?
From: James {- dot -} Whisstock {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU
Date: 2007-03-01

Subject: Re: RMSD of pairs of atoms?
From: ruben {- dot -} m {- dot -} buey {- at -} GOOGLEMAIL {- dot -} COM
Date: 2007-03-01

Dear Jan,
I think GROMACS can do that (www.gromacs.org):
____________________________________________________________________
g_confrms computes the root mean square deviation (RMSD) of two
structures after LSQ fitting the second structure on the first one.
The two structures do NOT need to have the same number of atoms, only
the two index groups used for the fit need to be identical. With -name
only matching atom names from the selected groups will be used for the
fit and RMSD calculation. This can be useful when comparing mutants of
a protein.
____________________________________________________________________

It will fit only those atoms specified in the index file,
independently on the name of the atom (you should use only C-alpha or
backbone atoms for the superimposition)

I hope this helps!

Best wishes,

Ruben

2007/3/1, Jan Lowe :
> Risking a potentially trivial question:
>
> Is there a program that will calculate the RMS of distances
> between specified (listed) atoms in two different structures?
>
> As far as I could see, LSQMAN will only compute same with same?
>
> Calculate RMSD of M1 A20 A30 A40 A50
> And M2 A20 A30 A41 A50
> Atom types
CA

> B-factor range used: -1000.00 - 10000.00 A2
> Nr of atoms to match : ( 3)
> Nr skipped (B limits) : ( 0)
>
> Many thanks,
> jan
>
> ------------------------------------------------------------------------------
> Jan Lowe email: jyl@mrc-lmb.cam.ac.uk
> Laboratory of Molecular Biology phone: +44 (0)1223 252969
> Medical Research Council fax : +44 (0)1223 213556
> Hills Road
> Cambridge CB2 2QH
> UK WWW: http://www2.mrc-lmb.cam.ac.uk/groups/JYL/index.html
> ------------------------------------------------------------------------------
>

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

Previous message:
Subject: Re: process SeMet labelled data
From: pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2007-03-01

Next message:
Subject: Re: RMSD of pairs of atoms?
From: James {- dot -} Whisstock {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU
Date: 2007-03-01