[PyMOL] Problem with Seleno-Cysteine

2002-08-06 Thread joergli 
Hi everybody

I have the structure of a Molybdo-CODH (CO-Dehydrogenase), which contains a
Seleno-Cysteine as Ligand for the active site cluster (see 1QJ2.pdb)
The residue b/388 is denoted as EYS in the pdb file.
In the cartoon representation, pymol does not display this part of the backbone
(I get a hole in the cartoon structure).
I can display this residue using show sticks, resi 388, and I can pick every
single atom, even the selenium.
Any idea how I can display the backbone without break?

Thanks
joerg

Internet et mail gratuit AltaVista http://www.altavista.fr

RE: [PyMOL] Problem with Seleno-Cysteine

2002-08-06 Thread DeLano, Warren 
alter eys/,type='ATOM'
sort

The problem is that, by default, PyMOL doesn't create ribbons for HETATMs 
(typically ligands and solvent).  With the above command, you're converting 
selenocysteine residues into regular atoms and sorting them into place so that 
they can be included in the ribbon.

Cheers,
Warren

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



 -Original Message-
 From: joer...@altavista.fr [mailto:joer...@altavista.fr]
 Sent: Tuesday, August 06, 2002 7:43 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Problem with Seleno-Cysteine
 
 
 Hi everybody
 
 I have the structure of a Molybdo-CODH (CO-Dehydrogenase), 
 which contains a
 Seleno-Cysteine as Ligand for the active site cluster (see 1QJ2.pdb)
 The residue b/388 is denoted as EYS in the pdb file.
 In the cartoon representation, pymol does not display this 
 part of the backbone
 (I get a hole in the cartoon structure).
 I can display this residue using show sticks, resi 388, and 
 I can pick every
 single atom, even the selenium.
 Any idea how I can display the backbone without break?
 
 Thanks
 joerg
 
 Internet et mail gratuit AltaVista http://www.altavista.fr
 
 
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[PyMOL] clipping planes

2002-08-06 Thread Nathaniel Echols 

I don't understand how these work at all.  Is there any straightforward 
way, given a structure's position and dimensions and the desired camera
position, to calculate the ideal position for the plane?   How does
PyMOL decide where to put the planes?  Right now I'm missing by a small
amount and atoms disappear randomly.

thanks,
Nat