OK, that's set for Jmol 12.1.24 and Jmol 12.0.23. I note that the
orientation and offset is off. It looks like PyMOL is centering the
coordinates on {0 0 0} rather than their actual molecular coordinates, but I
can't be sure if that is based on the protein or the surface, and it also
looks like there is a rotation, so I suspect that PyMOL is using the
current rotation of the model to generate the file. Thus, I'm not sure this
is going to be satisfactory. But the surface looks pretty good (despite the
poor resolution), and I'm able to strip out all the unnecessary repetitive
vertices that PyMOL generates.
See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Good luck!
Bob
On Tue, Nov 23, 2010 at 1:47 PM, Robert Hanson <[email protected]> wrote:
> Jmol just hasn't been set up to read OBJ files written in quite that format
> (where the vertices and faces are intermixed that way). Please send me the
> file; I'll fix it in short order.
>
> Bob
>
>
> On Tue, Nov 23, 2010 at 1:00 PM, Alexander Rose <
> [email protected]> wrote:
>
>> Hi,
>>
>> I tried to view obj files exported from pymol but could not get it to
>> work. The obj file from pymol looks reasonable, i.e.
>>
>> # file: pymol.obj
>> v 9.775413 -10.004283 -3.190735
>> v 9.996734 -10.529106 -3.207321
>> v 9.653004 -10.796073 -2.960678
>> vn -0.552027 -0.351046 -0.756328
>> vn -0.541946 -0.102013 -0.834199
>> vn -0.554205 -0.070096 -0.829424
>> f 1//1 2//2 3//3
>> v 9.147324 -10.091957 -2.762634
>> v 9.775413 -10.004283 -3.190735
>> v 9.653004 -10.796073 -2.960678
>> vn -0.329337 -0.334825 -0.882853
>> vn -0.552027 -0.351046 -0.756328
>> vn -0.554205 -0.070096 -0.829424
>> f 4//4 5//5 6//6
>> ... and more
>>
>> I tried it with some example file (a cube)
>>
>> # file cube.obj
>> v 1 1 1
>> v 1 1 -1
>> v 1 -1 1
>> v 1 -1 -1
>> v -1 1 1
>> v -1 1 -1
>> v -1 -1 1
>> v -1 -1 -1
>> f 1 3 4 2
>> f 5 7 8 6
>> f 1 5 6 2
>> f 3 7 8 4
>> f 1 5 7 3
>> f 2 6 8 4
>>
>> which works when load it with 'isosurface OBJ "/path/to/file.obj"', just
>> opening it with the open gui in the application does not work (12.1.23)
>>
>> Do you experience the same behavior? Can you point me to some pdb for
>> which jmol reads the exported obj surface?
>>
>>
>> Best
>> Alex
>>
>>
>>
>>
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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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Tap into the largest installed PC base & get more eyes on your game by
optimizing for Intel(R) Graphics Technology. Get started today with the
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