RE: [PyMOL] Separate surfaces

[DeLano, W. <wa...@su...>]

Jacob,

	It look to me like you've found a bug in PyMOL with the manual =
approach.  What's happening is that the result of a subsequent ignore =
command isn't updating the surface which was created before it.  The =
scripted behavior is correct, since all geometric objects should reflect =
the current state of the atom flags.

	The trivial fix to this kind of problem is to split all of the =
molecules into different objects and the create the surfaces =
independently.  In this case, use three objects instead of two.  That =
way you can ignore the "flag ignore.." command and only show surfaces on =
the proteins.

	Also note that if you're planning to move objects with surfaces =
attached, use the "object" parameter in the translate command.  =
Otherwise, PyMOL will have to recalculate the surface for each frame.

   translate [1,0,0],object=3D'A+amp'

or

   cmd.translate([1,0,0],object=3D'A+amp')

Also note that

  reset object=3D'A+amp'=20

will restore the object's original position.

Cheers,
Warren
=20
--
mailto:wa...@su...
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 FAX:(650)-266-3501



> -----Original Message-----
> From: Jacob Corn [mailto:jc...@uc...]
> Sent: Monday, January 20, 2003 1:36 PM
> To: pym...@li...
> Subject: [PyMOL] Separate surfaces
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> Hi all,
> It's possible that I've run into a bug/undocumented feature, but I'd=20
> like to see if anyone has a solution to the following problem.
> I'm working on a movie script that will (in part) make two separate=20
> surfaces for each subunit in a dimer (excluding a drug bound between=20
> the subunits), then split the monomers apart and zoom into a drug=20
> binding site. However, I'm running into some problems when I try to=20
> create the separate surfaces.
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> In plain english, what the script does is create two objects, one=20
> containing one subunit (B), and the other containing the=20
> other subunit=20
> AND the drug (A) (when I split the monomers apart I want the drug to=20
> follow one monomer). I then calculate the surface for subunit B, flag=20
> everything that's not subunit A as ignore, then calculate the surface=20
> for subunit A.
> If I input each line separately, the script works perfectly and I get=20
> two separate surfaces around each subunit and no surface around the=20
> drug. But if I run the script from the PyMOL command line or=20
> copy/paste=20
> the whole script at once into the command line, only subunit=20
> A shows a=20
> surface. The drug (correctly) does not have a surface, but (from the=20
> output in the terminal) it looks like PyMOL isn't even calculating a=20
> surface for subunit B.
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> Any ideas would be greatly appreciated.
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> Below are the relevant lines of the script:
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> ## make all of the objects we'll need
> cmd.create("A+amp+drug","a// or l/1/ or d//")
> cmd.create("B+amp","b// or l/2/")
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> cmd.select("drug","d//")
> cmd.select("A+amp","d// or l/1/")
> cmd.select("none")
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> cmd.delete("lc03")
> cmd.orient()
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> ## color it up
> cmd.color("orange","A+amp+drug and A+amp")
> cmd.color("wheat","B+amp")
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> ## let's show separate surfaces for each subunit
> cmd.show("surface","B+amp")
> cmd.flag("ignore","not A+amp","set")
> cmd.show("surface")
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> Many thanks,
> Jacob
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