Hi Elaine, Thanks a lot, molmap did the trick. With surface I¹m getting error 11, regardless how I specify the model/atoms. Before, I was trying to simply use MSMS surface (from the Action menu), but that would pick only a subset of points. Best, Karolina On 7/27/16, 5:32 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
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 ³cannot² (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 ³surface #1² didn¹t 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 ³molmap² 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. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.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 Jul 27, 2016, at 2:25 PM, Michalska, Karolina M. <kmichalska@anl.gov> wrote:
Hi,
I have a precalculated cavity represented as a grid in the pdb format, where ³atoms² 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