[Chimera-users] color surface based on NMR Order parameters

[Elaine Meng]

Hi Lalit,
Very similar to the reply I just sent to Wei:  you can create a custom attribute or property and assign the values to atoms or residues.  Then you can color the structure (including atoms, ribbons, surfaces) by those values.

To create a custom attribute, you create a simple text file and then read it in using the Define Attribute tool (in menu under Tools... Structure Analysis) or the command "defattr". The attribute file format is described here, and some example files are linked:

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html>

Then you can do the coloring with the Render by Attribute tool (under Tools... Structure Analysis):
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>

Besides colors, the values can be shown with sphere sizes or "worms".  You can also show the values as labels, as mentioned in the reply to Wei:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-June/005249.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 Jun 7, 2010, at 2:11 PM, lalit.deshmukh at huskymail.uconn.edu wrote:

> Hello,
> 
> I like the 'surface color ' feature in Chimera. I think, right now, the
> surface can be colored by radius, height, volume data and so on..
> 
> Is it also possible to color the surface  based upon the NMR order
> parameters or intensity ratios (it will be an Excel file containing just
> two columns: residue numbers and the respective parameter values)? Or this
> can be done in some other way?
> 
> Thanks in advance,
> 
> Regards,
> Lalit Deshmukh,
> University of Connecticut
> Storrs, CT 06269