[Chimera-users] rendering of custom annotation

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 25 11:17:31 PST 2016


Dear Helge,
Yes, you would only need to reformat your data slightly to make the “attribute file”  text format that can be read by Chimera.  Reading that file will assign the values as a residue attribute, and then you can easily color the residues (ribbons and/or atoms and/or surfaces) to show the values with either the Render by Attribute graphical interface or the “rangecolor” command.

Attribute file format and example files:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>

There are a few information lines at the top to say it is a residue attribute and what you want to name it, and the rest is just two columns preceded by tabs.  The first column will be residue identifiers just like you could use in the command line (for example  :26  for residue 26, :26.a  for residue 26 of chain A, etc. ) and the second column the value, in your case the number of hits.

Render by Attribute:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>

You would start Define Attribute (in menu under Tools… Structure Analysis) or use command “defattr” to read in your attribute file, and then the Render tool appears automatically, but you can also open it from the menu.

“rangecolor” command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>

For example, if you’d named your attribute “nhits”, you could use something like the following:

rangecol  nhits  min purple mid orange max yellow

(you can try this with “bfactor” instead of “nhits” if you haven’t made your attribute yet).  You can also give specific values instead of min/mid/max and lots of color names are shown here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortables.html#allcolors>

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 Jan 22, 2016, at 5:18 PM, Helge <helge.paternoga at googlemail.com> wrote:
> 
> Dear Chimera users,
> 
> I have some data, which contains numbers of hits for each given residue of a chain (in my case the 25S rRNA). The data consists of a table with two columns: residues and corresponding hits. I would now like to color each residue in Chimera, relative to the amount of hits, with the highest number always getting a defined color.
> 
> Is this possible?
> 
> best regards,
> 
> Helge




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