Hi Bill,
I would find it very useful to be able to retain the canonical PDB numbering
in a protein structure in my AMBER work. All this time, I have had to
remember what the conversions were (from AMBER to PDB and back), and due to
insertions/deletions it is not always a simple offset from the PDB numbers.
The most important few residues are easy to remember, but anything new
requires a lookup.
Christopher
-----Original Message-----
From: Bill Ross [mailto:ross_at_cgl.ucsf.edu]
Sent: Thursday, August 30, 2001 1:01 PM
To: nachman_at_hera.med.utoronto.ca
Cc: amber_at_heimdal.compchem.ucsf.edu
Subject: Re: residue numbering in dimers and trimers
The numbering scheme in the PDB file is such that it is easy to
indentify the monomers, but I know that tleap will number all the
residues sequentially, which can be a bit of a pain when one when
one wants to restrain the same residues in both monomers, and later
when translating the *.xyz or *.crd files back into *.pdb ones. I
wonder if there is any way to persuade tleap to preserve the
original
numbering scheme from the *.pdb file (or any numbering scheme which
will allow easy identification of the monomers).
It would require some programming, adding the pdb info to the
redidue unit on input & using it for savepdb and saveamberparm.
If anyone wants to do it, I'll advise & incorporate the code
into the release.
Bill Ross
Received on Thu Aug 30 2001 - 11:30:47 PDT
