[Chimera-users] Surface not including all molecules?

Tom Goddard goddard at sonic.net
Mon Dec 19 11:30:43 PST 2011

Hi Gustaf,

   Using the molmap command to create a density map of your molecules 
with resolution 2 Angstroms produces a good deal of space as shown in 
the attached picture.

     molmap #0 2 grid .2

The "grid .2" option says to make the density map grid spacing 0.2 
Angstroms which gives smoother appearance than the default which is to 
use 1/3 the resolution.


Gustaf Olsson wrote:
> It work, just a little to well. When I try I only get the "outer" surface for all molecules. Either trying to find a way to make the criteria more strict to leave more blank space "within" the sphere. Or divide the PYR residues into "clusters", creating surfaces for "aggregated" groups of molecules!
> But thanks a lot for the startingpoint!
> Best regards
> // Gustaf
> On Dec 16, 2011, at 19:37 , Elaine Meng wrote:
>> Hi Gustaf,
>> Your "structure" appears to be many separate small molecules.  In that case, you would probably have to tell Chimera that they should be enclosed together, since usually people would want different surfaces for the different molecules.  That could be done with the command surfcat.  Assuming you want all the atoms to be lumped together, something like:
>> surfcat mystuff #
>> surface mystuff
>> However, that surface calculation is likely to be problematic (there may be numerical failures) because the structure is very open, i.e. loosely packed: there are many holes and cavities if all those atoms are put together in one surface category.
>> When I tried it, I did get a surface plus a warning message.  One big surface was calculated successfully, but the calculation for other completely enclosed bubbles failed numerically.  The big surface does show many holes and a large interior cavity that is open to the exterior.  If you got that and it shows what you want, you are done.
>> However, if you needed the additional small bubbles, or you didn't get any surface at all when you tried this, you would need to try some tweaks to avoid the numerical failure.
>> Unfortunately a numerical failure is specific to everything (molecule, computer, all surface parameters, possibly even molecule orientation) and there is no one recipe to fix it in all situations.  Some things to try are changing the atomic VDW radii slightly and/or the molecular surface vertex density or probe radius.
>> For example, choose Favorites... Preferences, in Preferences go to Category: New Surfaces, and change settings before trying to calculate a surface.  To change vdw radii, could be something like command:
>> vdwdefine +.01
>> or to go back to default radii,
>> ~vdwdefine
>> The "split" command isn't relevant here, as it splits chains into separate models, but all the atoms in this structure are apparently chain "X".  If you did have multiple chains, but you wanted all the atoms to be in one surface, you still wouldn't want to split, because that would force calculation of a separate surface for each chain.
>> 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 Dec 16, 2011, at 12:54 AM, Gustaf Olsson wrote:
>>> Hello
>>> I'm trying to create a "cavity" model for visualization, I've done it before (a long time ago) and it worked great. But this time I'm having some problems. When trying with all molecules, I got some error regarding the calculation, so I split the model up into pieces and now it almost works.
>>> The problem I'm having is when I try creating a surface of one of the molecular species, I only get three "blobs" and not one big surface for all molecules. Any suggestions are most welcome.
>>> Don't know if it works, but I'll attach the PDB file for the molecules not being displayed as a surface properly.
>>> <shell_pyr.pdb>
>>> ______________________________
>>> Gustaf Olsson
>>> p://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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