[Chimera-users] user-defined attributes

Watson, Lisa Lisa.Watson at ucsf.edu
Wed Jan 5 15:20:54 PST 2011

Hi Elaine,

I am trying to create some figures using Chimera.  I used "define attributes" to color my protein structure according to values from data I generated.  Now I would like to manipulate the heatmap color scheme as well as to manipulate the threshold for the various colors.  Could you give me some tips on how to do this, or better yet, is there a time I can stop by your office to learn how to do this?

From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Thursday, August 26, 2010 8:17 PM
To: Watson, Lisa
Cc: chimera-users at cgl.ucsf.edu BB
Subject: user-defined attributes

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.

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