[Chimera-users] Surface representation
meng at cgl.ucsf.edu
Wed Jan 23 20:58:47 PST 2008
> 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.
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
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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