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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 > > ====================================================================