Also MUSTANG (multiple structural alignments) can be configured to output such data.
http://www.cs.mu.oz.au/~arun/mustang/
J
Ruben Martinez-Buey <[log in to unmask]> wrote:>
> 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 <[log in to unmask]>:
>> 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: [log in to unmask]
>> 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
>>
>> ------------------------------------------------------------------------------
>>
--
Professor James Whisstock
NHMRC Principal Research Fellow / Monash University Senior Logan fellow
Department of Biochemistry and Molecular Biology
Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia
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+613 9905 4699 (Fax)
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