VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 21 2007 - 15:24:04 CDT

Nicolas,
  You cannot presently modify the bond determination criteria on-the-fly,
but you can interactively edit the bonds and cause VMD to re-analyze
the structure on-the-fly. You could also use psfgen or autopsf to
build a complete structure and load a PSF with your PDB which would
more permanently address the issue. I plan to add some features that'll
allow more flexible automatic bond determination criteria soon in support
of people that work with very unusual structures that combine
silicon nanodevices and biological molecules, that would likely
help in cases like yours as well.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 21, 2007 at 02:14:23PM -0600, Nicolas Sapay wrote:
> Thanks for the fast answer,
>
> I have tried the selection text "residue $res" as you have suggested but
> the problem was still there. So, I have re-rechecked my pdb file.
> Apparently, a bond between the O1 and the P1 of the 200the lipid is not
> recognized by VMD. Lipid 200 is thus considered as 2 different residues.
> Same thing probably happened to 3 other lipids. That would explain why I
> have 4 more residues that expected. The problem is probably solvable if
> I find a way to modify the VMD criteria that define bonds.
>
> Nicolas
>
> Axel Kohlmeyer wrote:
> >On Fri, 21 Sep 2007, Nicolas Sapay wrote:
> >
> >
> >nicolas,
> >
> >
> >NS> 5 set sel [ atomselect $molid "$seltext" ]
> >NS> 6 # Retrieve the 'residue' number of the selection
> >NS> 7 set reslist [ lsort -integer -unique [ $sel get residue ] ]
> >NS> 8
> >NS> 9 # Assign a new 'resid' to each residue of the selection
> >NS> 10 foreach res $reslist {
> >NS> 11 # Do a temporary selection
> >NS> 12 set tmpsel [ atomselect $molid "$seltext and residue
> >NS> $res" ]
> >
> >please note, that in this case you overwrite only the resids
> >of those atoms that are in the selection, so parts of the same
> >residue may have different resids after the procedure.
> >if you want to overwrite the resid of all atoms in a given residue,
> >just use the selection text of "residue $res".
> >
> >NS> 13 $tmpsel set resid $start
> >NS> 14 $tmpsel delete
> >NS> 15 # Increment the new resid
> >NS> 16 incr start
> >NS> 17 }
> >NS> 18 $sel delete
> >NS> 19 return
> >NS> 20}
> >NS> #======================================
> >NS> However, the proc doesn't work with a simple system of 214 identical
> >NS> residues (it's a membrane bilayer). When I use the 'residue' keyword
> >at NS> line 7, I obtain a list of 218 'residue' which is wrong. But when I
> >do NS> the same thing using the 'resid' keyworkd, I obtain a correct list
> >of NS> 214 'resid'. Why do the 'residue' keyword give me 4 more residues?
> >(When NS> I do the renumbering, the resids start to be wrong at 200)
> >
> >please check, whether those resids have been actually overwritten.
> >see above.
> >
> >cheers,
> > axel.
> >
> >NS>
> >NS> Thanks for your help. I hope I'm not too confusing with all this
> >NS> 'residue' and 'resid'
> >NS>
> >NS>
> >NS>
> >NS> Nicolas
> >NS>
> >NS>
> >
> >
> 

-- 
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