VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 17 2008 - 09:24:55 CDT

Hi,
  Yes, these options are only available via VMD scripting, however
you can invoke your own scripts with the "-e" flag, and you can pass
in command line parameters to your script with the "-args" flag.
Your original question didn't mention the issue of launching from
command line so I wasn't aware that this was an important
consideration for you. If you want to send me the PDB file,
please gzip it up and email it to me (not VMD-L, just me..)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 17, 2008 at 03:14:39PM +0200, Sergey Ivanov wrote:
> It's that exactly what i want if it would work... With PSF i would
> deal in future but now have a series of troubles:
> 1) These options work only in vmd interpreter and they are not a
> command line options. But it wold be great to change \shell\command
> subkey in windows registry for vmd.exe (i have windows client as you
> guess).
>
> 2) After generatinng by this script it shows:
> Info) Analyzing structure ...
> Info) Atoms: 1208
> Info) Bonds: 12 (!!!!!!!!!!!!!!!!!!!!11- i know exactly what bonds
> it found but why???)
> Info) Residues: 1201
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 1201 Protein: 0 Nucleic: 0
> My PDB-file consists only of HETATM and CONECT sections. I would
> attach it but your mail-server don't support it as i understand.
>
> 2008/7/15 John Stone <johns_at_ks.uiuc.edu>:
> >
> >
> > Hi,
> > I agree that Axel's suggestion of generating a PSF is a generally
> > cleaner way of specifying bonds for use in VMD. If you feel the need
> > to continue using the PDB CONECT records to specify bonds (remember they
> > were only intended for "special" bonds, not for all bonds, which is why
> > VMD is also doing a distance-based bond determination), you can
> > workaround your present difficulties by loading the files with an extra
> > option:
> > mol new foo.pdb autobonds off
> >
> > That will prevent VMD from performing the additional distance-based
> > bond search in addition to reading the special bonds (in your case,
> > all of them) from the PDB CONECT records.
> >
> > I think Axel's suggestion is the better solution, but I offer
> > this as a shortcut in case you're time-constrained.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Tue, Jul 15, 2008 at 12:20:53PM -0400, Axel Kohlmeyer wrote:
> >> On Tue, 15 Jul 2008, Sergey Ivanov wrote:
> >>
> >> SI> Hello, developers!
> >>
> >> hi serge,
> >>
> >> SI> I want use VMD program for visualization of rahter beads on mesoscopic
> >> SI> level. In input for VMD i use PDB format with my own meaning of
> >> SI> "molecules" and "bonds". And respectivetly distance units has own
> >> SI> meanings.
> >> SI> I've tested PDB file (see attach) and found out that many bond plugged
> >> SI> to model from "nowhere"... Every "molecule" has not more then 3 bonds
> >> SI> with other ones accordingly to file but i see i quite other picture
> >> SI> and errors through loading:
> >> SI>
> >> SI> MolAtom xxx: Exceeded maximum number of bonds (12)
> >> SI>
> >> SI> Can you suggest workaround for me? As i understand from log:
> >> SI>
> >> SI> Info) Determining bond structure from distance search ...
> >> SI>
> >> SI> - it must be something that determines bond from exactly PDB file and
> >> SI> not "from distance"
> >>
> >> how do you specify bonds within a PDB file?
> >> which version of VMD are you using?
> >>
> >> recent versions of the PDB format reader try to read CONECT records
> >> and interpret them as bonds, but that requires your pdb file to
> >> conform to the PDB standard.
> >>
> >> the simpler way to specify bonds explicitly (and cleaner in my opinion)
> >> is to write a .psf format file. the NAMD tutorials have some explanation
> >> of the PSF format. you don't have to generate a complete .psf file. for
> >> visualization purposes only the atoms and bonds info are needed (and
> >> used).
> >>
> >> with the very latest VMD you should also be able to tell VMD to not
> >> try to guess bonds when loading from the command line prompt.
> >> please check the documentation.
> >>
> >> cheers,
> >> axel.
> >>
> >> SI>
> >> SI> --
> >> SI> Sergey Ivanov
> >> SI>
> >>
> >> --
> >> =======================================================================
> >> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> >> Center for Molecular Modeling -- University of Pennsylvania
> >> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> >> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> >> =======================================================================
> >> If you make something idiot-proof, the universe creates a better idiot.
> >
> > --
> > 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
> >
>
>
>
> --
> Sergey Ivanov 

-- 
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