[Chimera-users] preserving the serial numbering

George White gwcombio at gmail.com
Tue Jun 28 08:16:08 PDT 2011

Dear Eric,

Thank you so much for your quick response. We were using the minimization
routines in Chimera, and needed consistency in the atom numbering to
integrate with other components of our application.


On Mon, Jun 27, 2011 at 6:18 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi George,
> The short answer is no.  Generally speaking, unless your structure is
> unmodified (in which case, why not use the original file?) there is no way
> to write a standard-conformant PDB file while preserving original serial
> numbers.  Let's say you opened a structure, added hydrogens, and wanted to
> write it out with unchanged serial numbers.  Well, the hydrogens are going
> to have serial numbers larger than any heavy atom, so since they will be
> written along with their residue-mates in the file (else TER card
> conventions would be violated), the serial numbers will not be... serial.
> Nonetheless, I can imagine scenarios where you would be willing to ignore
> the not-strictly-legal nature of such a file, so I'll add a feature-request
> ticket to the Chimera Trac database with you on the recipient list.  If
> anyone else would also like to be on the notification list, send me an
> email...
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> On Jun 27, 2011, at 5:14 PM, George White wrote:
> Hi,
> I am wondering is there any way to write a pdb from Chimera that preserves
> the original atom serial numbering of the input pdb. Chimera seems to apply
> its own renumbering (i.e. making the number of the 1st atom #1 etc.) .
> Thanks in advance,
> George
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> Chimera-users at cgl.ucsf.edu
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