Alexander,
Glad to hear it is that simple. I do think you should report it as a bug to
PyMol, that they are outputting surface data that depends upon model
rotation. Does it also depend upon zoom?? That seems rather inappropriate to
me.
in Jmol, the following gets you there:
load xxxx.pdb
isosurface OBJ xxxxx.obj offset @{ {*}.xyz }
That is, move the isosurface to the protein, not the protein to the
isosurface.
It should be interesting for you to compare PyMOL's surfaces to Jmol's. I
don't think that's ever been done. From what I can see, the closest to that
in Jmol would be
isosurface select {protein} ignore {not protein} molecular
that is, a surface at the van der waals radius that is a rounded out form of
isosurface select {protein} ignore {not protein} sasurface 0
But they aren't exactly that, either, so perhaps PyMOL is adding hydrogen
atoms first, then doing the calculation?
I have no idea how PyMOL creates the troughs for the molecular surfaces.
Anyway, it's not a typical solvent-accessible surface, which would be
considerably larger. What's the PyMOL command that gives this?
Bob
On Wed, Nov 24, 2010 at 9:17 AM, Alexander Rose <[email protected]
> wrote:
> Hi Bob,
>
> I tried it and think you're right about PyMOL centering on {0 0 0}.
>
> Here is what I did:
>
> PyMOL> load 3dqb.pdb
> PyMOL> show surface
> PyMOL> save 3dqb_sas.obj
>
> Note: I did not move the protein in PyMOL
>
> Jmol> load auto "file:///path/to/3dqb.pdb"
> Jmol> isosurface OBJ "file:///path/to/3dqb_sas.obj"
>
> This shows the surface somewhat translated so I followed your idea about
> centering on {0 0 0}
>
> (editconf is a tool from the GROMACS suite, but you can probably do it with
> Jmol to)
> editconf -f 3dqb.pdb -o 3dqb_c.pdb -center 0 0 0
> Jmol> load auto "file:///path/to/3dqb_c.pdb"
> Jmol> isosurface OBJ "file:///path/to/3dqb_sas.obj"
>
> This shows the surface and the protein correctly superimposed
>
> The files I used and created:
> http://dl.dropbox.com/u/3778149/3dqb.tar.gz
>
>
> While this solves my problem, I am not completely satisfied. When I want to
> compare some PyMOL generated surfaces with other surfaces in Jmol (created
> by Jmol or yet another tool) I need to change my pdb files, but I would
> rather do it in the PyMOL-surface-pipeline.
>
> Manipulating the pdb file before creating the surface with PyMOL does not
> work because the PyMOL obj has no relation to the pdb coordinates. So the
> manipulation can only take place after the obj is created. I thought about
> translating the coordinates in the obj file. There basically three entries:
> v for vertices, vn for normal and f for faces. f can be ignored, because
> that are just indices to v or vn entries. v could be translated just be
> adding the appropriate translation vector. For vn I am not so sure, but
> Google tells me that using the inverse of the transformation matrix is the
> way to go.
>
> Is there a way to translate an isosurface? I did not find anything in the
> docs, but you never know. A 'translation vector' parameter for loading
> isosurfaces would be nice.
>
>
>
> Best
> Alexander
>
> ----- Ursprüngliche Mail -----
> > Von: "Robert Hanson" <[email protected]>
> > An: [email protected]
> > Gesendet: Dienstag, 23. November 2010 23:30:55
> > Betreff: Re: [Jmol-users] obj surface files exported from pymol
> > 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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> > Jmol-users mailing list
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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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> > grabs.
> > http://p.sf.net/sfu/intelisp-dev2dev
> > _______________________________________________
> > Jmol-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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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
------------------------------------------------------------------------------
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