[Chimera-users] Surface representation

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 23 20:58:47 PST 2008

> Hi,
> I would like to know if there is a way to build a surface  
> representation from a pdb file of a dummy atom saxs model in  
> chimera.  The file consist only of CA atoms. I could simulate this  
> by increasing the vdw radius but the model becomes way to big.
> Thanks
> James

Hi James,
You can use Multiscale Models to make a contour surface that encloses  
the "atoms."  The tricky part may be adjusting the contour surface  
parameters to get the desired smoothness and enclosed total volume.

At least in my tests, Chimera did not like the columns in your file  
after the B-factor column, so I made a version with those removed and  
opened it with "File... Open" before proceeding.  I will send you  
that file in a separate message.

(1) for purposes of comparison to the surface, I displayed the atoms  
as spheres with the radius 3.75 (this value was given in comments in  
the file) using the following commands:

setattr a radius 3.75
rep sphere

You can show the command line with Favorites... Command Line.

(2) started Multiscale Models (under Tools... Higher-Order  
Structure), clicked the "Make models" button near the bottom.  This  
generates the contour surface but hides the spheres.  To also show  
the spheres, Ctrl-click on the surface to select it, and then in the  
"Style" line of the dialog, choose "Show also.. Spheres".  To see  
spheres inside the surface, make it transparent; set Transparency to  
some fraction, say 0.3.

(3) Then you can fiddle with the contour surface parameters in the  
Multiscale Models dialog.  Many are hidden but can be shown by  
checking the box next to "..."   I got a fairly decent enclosure of  
the spheres with all default parameters except setting the "Threshold  
atom density" for "CA only" to 0.0006 instead of the default 0.002.   
You could also fiddle with the smoothing parameters and resolution if  
that is not good enough.

If you have some idea of what total volume the surface should  
enclose, that can be evaluated with Measure Volume and Area (under  
Tools... Volume Data).

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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