[Chimera-users] Surface rendering

[George Tzotzos]

Hi Tom,

Many thanks for this. Much appreciated.

Thanks also to Elaine for her suggestions.

Have a good weekend

George

On Jul 6, 2012, at 6:41 PM, Tom Goddard wrote:

> Hi George,
> 
>   You might want to use the "molmap" command to create a Gaussian surface instead of a solvent excluded surface.  For example if _clusters.pdb is model #2 and you want a 5 Angstrom resolution surface use:
> 
>     molmap #2 5
> 
> This never fails.  It sums a Gaussian centered at each atom and computes a contour surface.
> 
>     Tom
> 
>> Hi everybody,
>> 
>> I'm using SiteComp to detect differences in binding affinities between two similar structures. The _clusters.pdb file produced by SiteComp is a standard PDB file in which the grid points corresponding to the difference clusters are represented by hydrogen atoms. They can be treated as any molecule in Chimera.
>> 
>> Usually I find it useful to represent them as a mesh surface. Usually, I load in Chimera the protein.pdb, the ligand.pdb and the _clusters.pdb. After this, I select the _clusters.pdb and show it as mesh or solid using Actions-> Surface. In some cases, I fail to render the surface, or to be precise only one part of the clusters is rendered.
>> 
>> I understand that this is a frequent problem with this type of discontinuous pdb. I'm attaching one such file and I would be grateful for any help
>> 
>> Best regards
>> 
>> George
>> 
>> 
>> 
>> 
>> 
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> 
> 

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