[Chimera-users] precalculated void representation as surface

Michalska, Karolina M. kmichalska at anl.gov
Thu Jul 28 08:07:27 PDT 2016

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.

On 7/27/16, 5:32 PM, "Elaine Meng" <meng at 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.
>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>
>> 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

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