DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the
pairwise alignment function. It is all automatic and will give you the
lowest rmsd. Note, however, that it will omit parts that are very different
for calculation.
Within CCP4, SUPERPOSE or COOT can also do that. You need to specify the
residues you want to use for calculation for the lsq fit function.
Regards,
Clement Angkawidjaja, PhD
Specially Appointed CMP Assistant Professor
Graduate School of Engineering
Osaka University
2-1 Yamadaoka GSE Commoon East 8F
Suita-shi, Osaka 565-0871, Japan
Tel/Fax +81-6-6879-4580
http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html
///////////////////////////////////////////////
G30 Chemistry/Biology Combined Major Program
http://cmp.sci.osaka-u.ac.jp/CMP/
-----Original Message-----
From: E rajakumar
Sent: Monday, November 15, 2010 6:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question on calculation of RMSD
Dear All
I have two structures of homo-dimeric protein complex with different DNA.
I want to calculate RMS deviation between second monomer from these two
complexes by fixing superposed first monomer.
This I require to know what is the effect of DNA on relative orientation of
two monomers in the dimer.
Previously I was using MOLEMAN2 to do this calculation.
Please can you suggest me any other program to do this calculation.
Thanking you
Raj
E. Rajakumara
Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering
Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266
(Mobile)
