[Chimera-users] code or psuedo code for unit cell packing

Bennion, Brian Bennion1 at llnl.gov
Wed Sep 24 09:41:20 PDT 2014


Thank you Elaine,

Perhaps I wasn't clear enough.  I can use the smtry operations found in the the REMARK 290 records to create what appears to be an individual monomer of a protein in a separate unit cell (2FDN).  With this pdb there are 8 monomers per unit cell, however, without selecting packing I just get 8 monomers in 8 unit cells.

You state that the packing option chooses the copy of the each chain that puts its center within the outline of a single unit cell box.  Can you show me what that code looks like?  I just want to understand what the translation/rotation operations are...

Brian



________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Wednesday, September 24, 2014 9:27 AM
To: Bennion, Brian
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] code or psuedo code for unit cell packing

Hi Brian,
The symmetries in the PDB file define the possible positions of multiple copies of a chain in the repeating array of unit cells.  See the documentation for descriptions of which matrices from the PDB file are used (depends on your own settings in the Options). The packing option chooses the copy of each chain that puts its center within the outline of a single unit cell box.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



On Sep 24, 2014, at 8:38 AM, Bennion, Brian <Bennion1 at llnl.gov> wrote:

> Hello
>
> I found the unit cell gui to be very useful  recently.  However I am curious about how the "pack into unit cell" option works.  What information in the pdb header is used to translate/rotate a set of monomers each in an individual unit cell and pack them back into the "original cell".
>
> Thanks for any help
> Brian




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