From: Sergio Anis (sergioanis_at_ispwest.com)
Date: Fri Sep 16 2005 - 11:20:10 CDT

thanks;
have a great weekend
Sergio

----- Original Message -----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: 9/16/2005 9:17:13 AM
To: sergioanis_at_ispwest.com
Cc: vmd-l_at_ks.uiuc.edu;jcc67_at_caece.net
Subject: Re: vmd-l: writing pdb

>
> Hi Sergio,
> It isn't done yet, but it's something I'm currently working on..
> I'll let VMD-L know when I have a version available for you to test.
>
> John
>
> On Thu, Sep 15, 2005 at 10:52:21PM -0400, Sergio Anis wrote:
> > hi John,
> >
> > welcome back.
> > does the new version load the pdb according to the conect records? from wich
> > version? (i have 1.8.3)
> >
> > thanks,
> > Sergio
> >
> > -------Original Message-------
> >
> > From: John Stone
> > Date: 09/15/05 13:20:27
> > To: Sergio Anis
> > Cc: vmd-l_at_ks.uiuc.edu; Jen-Chang Chen
> > Subject: Re: vmd-l: writing pdb
> >
> > Hi,
> > I've just returned from a conference and am still catching up on emails...
> > The PDB plugin used by all of the previous versions of VMD ignores the
> > CONECT
> > records, so the CONECT records aren't the cause of your specific problem.
> > Most likely the issue is that you've got atoms clashing or structures with
> > an unusual scale. When you load a PDB file without a PSF file, VMD uses a
> > distance-based bond search, and so if you have an area with unusually high
> > atom density, you can get error messages like these. If you build a proper
> > structure with 'psfgen' and then load a matching PSF file into VMD, these
> > errors will go away.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Sep 14, 2005 at 04:06:48AM -0700, Sergio Anis wrote:
> > > i re-check the CONECT statements and found out some mistakes, there are
> > some 'dangling' atoms. i guess that they are responsible for the error
> > messages 'exceeded number of bonds' since the software is not able to tell
> > if they belong to the protein or the heterogroup.
> > >
> > > thanks for your help
> > > Sergio
> > >
> > > ----- Original Message -----
> > > From: Dow Hurst DPHURST
> > > Date: 09/13/05 16:16:12
> > > To: Sergio Anis
> > > Subject: Re: vmd-l: writing pdb
> > >
> > >
> > >
> > >
> > >
> > > Not necessarily, it depends on how the code is designed to interpret the
> > > PDB file. If no connectivity information is included in the PDB file and
> > > also if the program uses topology files as a reference, then you might not
> > > see anything or just unconnected dots. PDB is great for well defined
> > > proteins but can give problems with small molecules and so on.
> > > Dow
> > >
> > >
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078