Re: [PyMOL] Problem with Seleno-Cysteine

[Jörg Johannes]

Am Dienstag, 6. August 2002 18:33 schrieben Sie:
> 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.

Ok, thanks. That does well for now, but wouldn't it be nicer to include this 
"alter" setting as default for pymol, e.g. for ESY and MSE (Seleno- 
Methionine), so that the user does not have to set it himself every time
they appear? Just an idea, because I have seen those rather often in 
metallo-enzymes; but this was the first time I searched for the reason of the 
broken backbone...

joerg

RE: [PyMOL] Problem with Seleno-Cysteine

[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
> 
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