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Re: [ccp4bb] RMSD of pairs of atoms? |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 01 March 2007Subject: Re: RMSD of pairs of atoms? From: James {- dot -} Whisstock {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU Date: 2007-03-01 http://www.cs.mu.oz.au/~arun/mustang/ J Ruben Martinez-Buey > 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 >> >> ------------------------------------------------------------------------------ >> -- 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 +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile) CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 01 March 2007 |
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