If the molecule is big, you may be just running into the problem that the
resolution is low, because it is adjusted by default for 80x80x80 points.
You could try RESOLUTION 1.0 as a parameter.
On Sun, Jan 16, 2011 at 9:40 PM, Robert Hanson <[email protected]> wrote:
> Aya, what version of Jmol are you using? The equivalent of
>
> geosurface
>
> would be
>
> isosurface vanderwaals
>
> (with the desired select/ignore)
>
> Those should be closed surfaces.... Send an example, please.
>
> Bob
>
> On Sun, Jan 16, 2011 at 7:59 PM, Aya <[email protected]> wrote:
>
>> Hello there!
>>
>> I am having a hard time making solvent/molecular/sasurface generate closed
>> surfaces for the molecules I'm working with. I have even tried the
>> following:
>>
>> isoSurface surf1 select(selectedAtoms) ignore(not selectedAtoms)
>> molecular/solvent/sasurface;
>>
>> Which is better, but still pretty 'holy'. Geosurface is Perfect! Closed
>> surfaces and fast rendering. However, there is no ID set for the
>> geosurface, and when I add a new surface, the color of the previously
>> generated geosurface defaults to the color of the atoms. I'd like to add
>> and remove these surfaces as the user pleases.
>>
>> Do you think there is a way around this? A way I could write a script to
>> define a unique identifier for a geosurface? Or a new way to use the
>> isosurface? Or perhaps something else?
>>
>> Thank you kindly!
>> Aya
>>
>>
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>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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