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, <[log in to unmask]<mailto:[log in to unmask]>> 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:[log in to unmask]<mailto:[log in to unmask]>] Im Auftrag von sreetama das
Gesendet: Mittwoch, 13. August 2014 08:12
An: [log in to unmask]<mailto:[log in to unmask]>
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.
