[Chimera-users] Surface rendering

[Elaine Meng]

Hi George,
One more idea: just show the cluster as atoms in the sphere representation.  From your description, SiteComp makes them hydrogens, so that would initially just use the hydrogen radius in Chimera.  However, you could set the "VDW" radii (and thus sphere size) of those fake atoms to whatever value you like.  For example, if your cluster.pdb file is open as model 2, set the radii of its atoms to 2.5 angstroms:

rep sphere #2
vdwdef 2.5 #2

The atom spheres can't be shown as mesh, but you could make them transparent, for example:

color 1,0,0,.5 #2

Elaine

On Jul 6, 2012, at 9:43 AM, George Tzotzos wrote:

> 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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>>> 
>>> Chimera-users at cgl.ucsf.edu
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>> 
>> 
> 
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