My intent in my earlier response to Frances was to start a discussion
about whether there really are consistent policies numbering policies in
place and what people's experiences with those have been -- and whether
they serve the needs of the community at present. The limited feedback
so far is mixed. I think - as a previous poster has suggested - that
alot depends on who is working with your deposition. My own experience
with many different PDB staff members has illustrated a wide variance of
flexibility and style and 'sticklerness'. It seems that, at least, is
what other users are also finding.
FWIW, though not the intent of the topic, I think the PDB is a microcosm
just like any group of people in any organization. Some folks are more
ready/willing/able to work with people to solve problems, others aren't;
some are having a good day when you encounter them, some aren't. At no
time did we attempt to demand anything. We did, however, run into
unwillingness to find any middle ground. That was disappointing. Did we
adhere to what we were told we must in order to complete the deposition?
Yes. Do we think it best represented the work, in the context of the
field? No. But science and life goes on.
-Linda
Jens T. Kaiser wrote:
I have found the people at the pdb very helpfull and accomodating.
I think the key point is to /discuss/ the issue with them instead
of 'demanding' a certain way of deposition. The depositors may have their
reasons for certain namings, but the pdb has its reasons too, often based on
a much broader aplicability than the single user. I'm sure when the problem
and reasons are stated, a compromise can be found.
In this case I see no problem whatsoever naming the parts with different chain
names, whereas I see a problem deositing one chain with partly iverlapping
sequence numbers. Also the referencing of the sequnece database entries gets
simpler.
Just my 20 cents
Jens
On Monday 22 September 2008 06:23:16 Todd Geders wrote:
From the PDB:
Begin forwarded message:
From: Jasmine Young <[EMAIL PROTECTED]>
Date: September 22, 2008 7:48:30 AM CDT
To: Todd Geders <[EMAIL PROTECTED]>
Cc: [EMAIL PROTECTED]
Subject: Re: Non-sequential residue numbering?
Dear Todd,
We encourage depositors to use sequential numbering in the
coordinates. Using insertion code is discouraged. However depositors
can use numbering which matches to the numbering in sequence
database as long as the numbering is unique within a polymer chain.
Therefore we should be able to handle the numbering you have
mentioned below.
Jasmine
--
====================================================================
Jasmine Young, Ph.D.
RCSB Protein Data Bank
Department of Chemistry and Chemical Biology
Rutgers The State University of New Jersey
610 Taylor Road
Piscataway, NJ 08854-8087
Email: [EMAIL PROTECTED]
Phone: (732) 445-0103 ext 231
Fax: (732)-445-4320
====================================================================
--
Linda S. Brinen
Adjunct Assistant Professor
Dept of Cellular & Molecular Pharmacology and
The Sandler Center for Basic Research in Parasitic Diseases
Phone: 415-514-3426 FAX: 415-502-8193
E-mail: [EMAIL PROTECTED]
QB3/Byers Hall 508C
1700 4th Street
University of California
San Francisco, CA 94158-2550
USPS:
UCSF MC 2550
Byers Hall Room 508
1700 4th Street
San Francisco, CA 94158
