Andrew Martin's ProFit program is another option:
http://www.bioinf.org.uk/software/profit/doc/node11.html
Having fitted the structures using the ZONE and ATOMS commands to
specify which residues and atoms should be included in the fitting,
the RMS deviation may then be calculated over a different region of
the structure and/or a different atom set.
This is achieved using the RZONE and RATOMS commands. The syntax of
these commands is identical to that of the ZONE and ATOMS commands
described in Sections 8 and 9.
-Eric
-----Original Message----- From: E rajakumar
Sent: Monday, November 15, 2010 6:52 AM
To: [email protected]
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)
--
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Eric Bennett, [email protected]
Drawing on my fine command of the language, I said nothing.
-Robert Benchley
