[PyMOL] PDB changed CONNECT records

2007-09-06 Thread Mark A Saper
This was previously discussed in an archived email but I can't find  
it right now.  Does the setting connect_mode=0 use the CONECT records  
in the PDB file or not?  I think it does. Apparently in pdb code  
1ABE, the CONECT records were changed in a 2005 revision.  Two  
alternate sugar conformations are now interconnected when using the  
current 1ABE.  The old 1ABE (from 1993) seems fine.


Should setting connect_mode to 0 before loading PDB fix it?  I don't  
think it does.


Thanks,
Mark

_
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics, University of Michigan
930 N University Ave
Ann Arbor MI 48109-1055   U.S.A.

sa...@umich.edu(734) 764-3353fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html



Re: [PyMOL] PDB changed CONNECT records

2007-09-06 Thread Abhinav Verma
AFAIK setting connect_mode=1 strictly uses the CONECT records from pdb file
to draw bonds.

Cheers,
Abhi.



On 9/6/07, Mark A Saper  wrote:
>
> This was previously discussed in an archived email but I can't find it
> right now.  Does the setting connect_mode=0 use the CONECT records in the
> PDB file or not?  I think it does. Apparently in pdb code 1ABE, the CONECT
> records were changed in a 2005 revision.  Two alternate sugar conformations
> are now interconnected when using the current 1ABE.  The old 1ABE (from
> 1993) seems fine.
>
> Should setting connect_mode to 0 before loading PDB fix it?  I don't think
> it does.
>
>
> Thanks,
> Mark
>
>  _
>
> *Mark A. Saper, Ph.D.*
>
> Associate Professor of Biological Chemistry
>
> Biophysics, University of Michigan
>
> 930 N University Ave
>
> Ann Arbor MI 48109-1055   U.S.A.
>
>
> sa...@umich.edu(734) 764-3353fax (734) 764-3323
>
> http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
>
>
>
> -
> This SF.net email is sponsored by: Splunk Inc.
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>


Re: [PyMOL] PDB changed CONNECT records

2007-09-06 Thread DeLano Scientific
Mark,
 
set connect_mode = 0  is the default, and this uses both distance-based and
explicit (CONECT-based) connectivity.
 
set connect_mode = 1 uses only explicity connectivity
 
we don't have a connect_mode = 2 yet (forcing use of distance-based
connectivity only), so instead, you'll need to remove the errant CONECT
records from the "new & improved" pdb file or simple unbond the
mis-connected residues.
 
unbond ARA`307/, ARB`308/
 
Cheers,
Warren
 


  _  

From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Mark A Saper
Sent: Thursday, September 06, 2007 10:48 AM
To: Pymol
Subject: [PyMOL] PDB changed CONNECT records


This was previously discussed in an archived email but I can't find it right
now. Does the setting connect_mode=0 use the CONECT records in the PDB file
or not? I think it does. Apparently in pdb code 1ABE, the CONECT records
were changed in a 2005 revision. Two alternate sugar conformations are now
interconnected when using the current 1ABE. The old 1ABE (from 1993) seems
fine. 

Should setting connect_mode to 0 before loading PDB fix it? I don't think it
does.

Thanks,
Mark


_

Mark A. Saper, Ph.D.

Associate Professor of Biological Chemistry

Biophysics, University of Michigan

930 N University Ave

Ann Arbor MI 48109-1055 U.S.A.




sa...@umich.edu (734) 764-3353 fax (734) 764-3323

http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html




Re: [PyMOL] PDB changed CONNECT records

2007-09-06 Thread DeLano Scientific
Actually, upon closer look, the residue wasn't defined using the proscribed
PDB alternate location identifiers, so in fact, PyMOL itself is unable to
avoid misconnecting the atoms.
 
Thus, you'll need to use "unbond" either way.

  _  

From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano
Scientific
Sent: Thursday, September 06, 2007 11:24 AM
To: 'Mark A Saper'; 'Pymol'
Subject: Re: [PyMOL] PDB changed CONNECT records


Mark,
 
set connect_mode = 0  is the default, and this uses both distance-based and
explicit (CONECT-based) connectivity.
 
set connect_mode = 1 uses only explicity connectivity
 
we don't have a connect_mode = 2 yet (forcing use of distance-based
connectivity only), so instead, you'll need to remove the errant CONECT
records from the "new & improved" pdb file or simple unbond the
mis-connected residues.
 
unbond ARA`307/, ARB`308/
 
Cheers,
Warren
 


  _  

From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Mark A Saper
Sent: Thursday, September 06, 2007 10:48 AM
To: Pymol
Subject: [PyMOL] PDB changed CONNECT records


This was previously discussed in an archived email but I can't find it right
now. Does the setting connect_mode=0 use the CONECT records in the PDB file
or not? I think it does. Apparently in pdb code 1ABE, the CONECT records
were changed in a 2005 revision. Two alternate sugar conformations are now
interconnected when using the current 1ABE. The old 1ABE (from 1993) seems
fine. 

Should setting connect_mode to 0 before loading PDB fix it? I don't think it
does.

Thanks,
Mark


_

Mark A. Saper, Ph.D.

Associate Professor of Biological Chemistry

Biophysics, University of Michigan

930 N University Ave

Ann Arbor MI 48109-1055 U.S.A.




sa...@umich.edu (734) 764-3353 fax (734) 764-3323

http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html