Re: [PyMOL] Loading non-standard PDB file

[Holly Miller]

Warren,

Thanks for the quick reply!

>
>Right now PyMOL has pretty limited connectivity detection
> capabilities for "in-process" structures, which do not exhibit normal
> bond lengths and atom separations.   A workaround would be to passage
> the structure through energy minimization (using an external tool)
> before loading it into PyMOL (which will establish correct connectivity
> for the object) and to then load the original in-process coordinates as
> state 2 of the object.

I don't think that the structure has abnormal atom distances. Is it just
that the pdb file does not have HETATM or CONECT or other 'extras' 

>
>   Alternatively, is there any way you could use HETATM records (instead
> of ATOM) and include explicit CONECT records?

I think this would solve the problem. I tried to search for a program/script
that would do this and didn't find one. Seems like there should be many of
these.

Again, I am sorry for taking up your time on this simple problem but I want
to use PyMol and I have been struggling with this for a week now.


Cheers,
Holly
--


Holly Miller, Ph.D.  voice: 631 444-8018
Res. Asst. Prof. FAX:  631 444-7641
Dept. Pharm. Sci.http://www.pharm.sunysb.edu/faculty/miller/

SUNY Stony Brook mil...@pharm.sunysb.edu
Stony Brook, NY 11794-8651



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RE: [PyMOL] Loading non-standard PDB file

[DeLano, Warren]

Holly,

   Right now PyMOL has pretty limited connectivity detection
capabilities for "in-process" structures, which do not exhibit normal
bond lengths and atom separations.   A workaround would be to passage
the structure through energy minimization (using an external tool)
before loading it into PyMOL (which will establish correct connectivity
for the object) and to then load the original in-process coordinates as
state 2 of the object.

   Alternatively, is there any way you could use HETATM records (instead
of ATOM) and include explicit CONECT records?

   Before too long, PyMOL will have pattern-based connectivity
determination for normal PDB residues.

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: Holly Miller [mailto:mil...@pharm.sunysb.edu]
> Sent: Friday, March 08, 2002 10:57 AM
> To: PyMol Users
> Subject: [PyMOL] Loading non-standard PDB file
> 
> 
> Hi!
> 
> I am a new PyMol user. I want to look at an 'in progress' 
> structure from
> a collaborator. When I load the pdb into PyMol there are bonds between
> atoms that shouldn't be bonded. This is mostly (if not only) in the
> bound DNA part of the structure. Is it possible to change the 
> parameters
> by which the bonds are automatically calculated (if this is how it
> works) or some other way to fix this, other than clicking on 
> each wrong
> bond and deleting it (there are many).
> 
> I apologize for asking such a simple question.
> 
> Thank you,
> Holly
> 
> --
> __
> __
> 
> Holly Miller, Ph.D.  voice: 631 444-8018
> Res. Asst. Prof. FAX:  631 444-7641
> Dept. Pharm. Sci.
> http://www.pharm.sunysb.edu/faculty/miller/
> SUNY Stony Brook mil...@pharm.sunysb.edu
> Stony Brook, NY 11794-8651
> 
> **
> **
> 
>  Biomail--New references from Medline to your 
> e-mail account
> 
>   http://www.biomail.org
> __
> _
> 
> 
> 
> 
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