[Chimera-users] precalculated void representation as surface
meng at cgl.ucsf.edu
Wed Jul 27 15:32:30 PDT 2016
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:
(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:
> 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,
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