Re: [PyMOL] surfaces for molecules with non-standard VDW's

Thanks! That works.

In the past I had actually wanted to set solvent radius fairly large,  
but had poor luck getting the results I wanted. Now it seems to solve  
this particular problem. Go figure.

Richard


On May 22, 2007, at 10:53 AM, Tsjerk Wassenaar wrote:

> Hi Richard,
>
> What about
>
> set solvent_radius,3
>
> That seems to do the trick for me.
>
> Cheers,
>
> Tsjerk
>
> On 5/22/07, Richard Gillilan <re...@co...> wrote:
>>
>> In the past I have used PyMol pretty successfully to visualize low-
>> resolution x-ray solution scattering results in which each "atom" in
>> a pdb file is actually a large sphere (say 4-6 Angstroms)
>> representing some density.  I would use
>>
>>  >alter <molecule name>, vdw = 6.0
>>
>> to set the sphere sizes appropriately, then compute a surface using
>> the "surface" option in the "Show" pulldown of the appropriate  
>> object.
>>
>> Strangely, this seems to have quit working for me. When I select
>> surface, nothing happens, not even an error message.
>> It still works fine for older files I have, so it must be something
>> particular about the geometry of the object I have (it is a rather
>> sparse extended object). Anyone seen this kind of problem?
>>
>> File is included below:
>>
>>
>>
>>
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>
>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
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> The Netherlands
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