Thanks to the mailing list I came across this: http://www.ncbi.nlm.nih.gov/pubmed/24167157
The C code to compute is available on the link mentioned in the paper. Best wishes, George On Wed, Aug 13, 2014 at 8:01 AM, Eugene Krissinel < [email protected]> wrote: > It is probably Gesamt/SSM (Superpose in CCP4), or PDBeFold at EBI rather > than PISA -- Eugene > > On 13 Aug 2014, at 12:33, Eleanor Dodson wrote: > > I think PISA does this for you - it overlaps structural features and gives > an RMSD on those parts that fit and a useful list of matching residues. > You can run it from CCP4I or at PDBe. > > If you ant more than CA RMSD then you will need to select out the spans to > fit and use the LSQKAB overlap procedure > FIT MAIN RESi n n+m CHAIN A > MATCH RESI b b+m CHAIN C > > FIT …. > > etc > > for example - you can do that in the GUI > > Eleanor > > > On 13 August 2014 02:48, <[email protected]<mailto: > [email protected]>> wrote: > Dear Sreetama, > > I use an ancient superposition program which rejects all atom pairs > deviating more than 3 sigma and repeats this procedure until convergence. > It then reports the RMSD for all atoms and for the atoms deviating less > than 3 sigma. I find this an excellent method to separate the core from > variable loop regions. It also ensures a robust superposition of the cores, > ignoring variable loops. > > Best, > Herman > > Von: CCP4 bulletin board [mailto:[email protected]<mailto: > [email protected]>] Im Auftrag von sreetama das > Gesendet: Mittwoch, 13. August 2014 08:12 > An: [email protected]<mailto:[email protected]> > Betreff: [ccp4bb] RMSD between structures of homologous proteins > > Dear all, > When calculating the RMSD between structures of homologous > proteins, where there are large changes in the loop region(s), which RMSD > should be reported - an overall value which may be inflated due to the > deviations in the loops, or separate values for the core and loop regions? > What is the best way to calculate the RMSD for superposition of the cores > - should I prepare a separate PDB file by removing the coordinates of the > loop residues and then superpose? > > Thanks in advance, > Sreetama das, > PhD student, > Physics, IISc > > > > -- > Scanned by iCritical. > >
