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 <[log in to unmask]>
>>> Date: September 22, 2008 7:48:30 AM CDT
>>> To: Todd Geders <[log in to unmask]>
>>> Cc: [log in to unmask]
>>> 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: [log in to unmask]
>>> 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: [log in to unmask]
QB3/Byers Hall 508C
1700 4th Street
University of California
San Francisco, CA 94158-2550
USPS:
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