Making a New Structure?
Simon M. Brocklehurst
smb at bioch.ox.ac.uk
Mon Apr 29 05:46:56 EST 1996
Todd Charles Wood wrote:
> I am looking for a program that will read in PDB coordinates of
> the backbone of a protein and build onto that the sidechains
> that I specify. I want to use this "new" structure to do
> energy minimization on. Any suggestions?
> Todd Wood
> tcw3r at virginia.edu
NAOMI might do what you need - to give you an idea, here's how
you would build the sequence A K H at residue positions 14, 15 and
16 in the protein fold.
mutate 14 A
mutate 15 K
mutate 16 H
If your backbone coordinates have the right amino acid residue sequence
in the PDB file, you could instead use the command:
which would do everything in one go.
| ,_ o Simon M. Brocklehurst,
| / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry,
| \>> | University of Oxford, Oxford, UK.
| \\, E-mail: smb at bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/
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