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:
[log in to unmask]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)
