[Chimera-users] user-defined attributes

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 26 20:17:26 PDT 2010

Hi Lisa,
Yes, you could do exactly that same thing, and then what is shown as "bfactor" in the Render by Attribute dialog is really whatever values you put in the PDB file.

However, Chimera is even more flexible in that you can create your own custom attributes and assign their values with a different file, instead of having to edit the input PDB file.  An "attribute definition" file is a simple text file, and it is less limiting because you can have several different custom attributes at the same time, with whatever names you have assigned them (not necessarily "bfactor").  An attribute definition file is read in using the Define Attribute tool or the command "defattr."  A description of the format and links to several examples can be viewed here:


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

On Aug 26, 2010, at 4:21 PM, Watson, Lisa wrote:

> Hi Elaine,
> Is it possible to use the Render by Attribute function to color code a structure according to data values that can be entered for each residue?  In pymol this can be done by replacing overwriting b values with other data.
> Thanks,
> Lisa
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