[Chimera-users] precalculated void representation as surface

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 27 15:32:30 PDT 2016

Hi Karolina,
It is very difficult to answer questions like this without having the input file or a more complete description of what you mean by “cannot”  (looks bad?  error message?  if error message, what does it say??)  So I can only make guesses.

Maybe it is hard to specify the atoms... at least in my attempt to simulate the problem, even though the model was open as #1, command  “surface #1” didn’t work and I had to use this command instead:

surface #1@*

(without any space between the model number and @*)

If that fails to give a surface, another possibility is simulating a density map with “molmap” and then adjusting the isosurface of that density map, for example if you opened the fake PDB file as #3, a command something like:

molmap #3@* 1.0

Then you will get the Volume Viewer dialog with a histogram and slider you can drag to adjust the isosurface level.  The second number in the example command is an adjustable parameter and I do not know what value will work well with your file.  You should try different numbers and also take a look at what other options are available with molmap.

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 Jul 27, 2016, at 2:25 PM, Michalska, Karolina M. <kmichalska at anl.gov> wrote:

> Hi,
> I have a precalculated cavity represented as a grid  in the pdb format, where “atoms” are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface.
> I appreciate your help,
> Karolina

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