Eric,
PyMOL's "fuse" command will merge two distinct objects into a
one while forming a bond. For example:
fragment arg
move y,8
fragment glu
zoom
fuse arg/n, glu/o
delete arg
zoom glu
will create an arginine and a glutamine, and then copy the arginine into
the glutamine object, while forming a bond from the amino nitrogen in
ARG to the carbonyl carbon in GLU.
Cheers,
Warren
--
mailto:[email protected]
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: [email protected] [mailto:pymol-users-
> [email protected]] On Behalf Of Eric Hu
> Sent: Friday, October 10, 2003 2:05 PM
> To: [email protected]
> Subject: [PyMOL] make a bond from two different molecule
>
> Hi, I am using the newest pymol windows version. I
> need to make a bond between the protein and ligand
> since they form a covalent complex. When I use 'bond'
> command, pymol requires that two bonded atoms are in
> the same molecule. I have to load two molecules
> seperately in order to identify the interactions (e.g.
> hydrogen bond) between them. I wonder if I can unite
> them into one molecule afterwards to use 'bond'
> command. Or there is a better way to do it. Thanks!
>
> Eric
>
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