VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 08 2005 - 16:36:29 CST

Andrea,
  Try the new 1.8.4b4 builds I just posted today and let me know if they work
better "out of the box" than the previous build did for your particular
structures:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 05, 2005 at 10:24:16AM +0100, andrea spitaleri wrote:
> Hi John,
> thanks for your kind answer. As a debugger, I can try it the new vmd-build.
> Thanks
>
> andrea
>
> John Stone wrote:
>
> >Andrea,
> > I've got a new VMD build that merges in CONECT records with the
> >automatic distance-based bond search now. The new code will also let
> >you disable either of the PDB CONECT records or the automatic bond search
> >so you can override this behavior if you want. Let me know if you want to
> >try this new build, it's not posted on the web yet.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Nov 29, 2005 at 10:22:52AM +0100, andrea spitaleri wrote:
> >
> >
> >>Hi all,
> >>thanks for fixing this "issue". However, I have noticed another
> >>"problem". I have got a file.pdb and it is visualised properly. After
> >>feeding it to the gromcas tools (such as pdb2gmx or editconf ), the
> >>terminus aminoacid seems unbonded. In fact, if I select "protein", the
> >>terminus residue is not selected. That's strange since in gromacs
> >>topology file the C-N bond is still there. The bond distance is within
> >>the cutoff, I guess.
> >>
> >>
> >>Regards,
> >>
> >>andrea
> >>
> >>John Stone wrote:
> >>
> >>
> >>
> >>>Hi,
> >>>I think that doing what others suggested is the best thing in the short
> >>>term, but I wanted to mention that I now have CONECT record reading in
> >>>the
> >>>VMD PDB reader, and I'm working on making it do the right thing since
> >>>most
> >>>PDB files only have CONECT records for a small subset of the bonds in the
> >>>system (usually only the unusual ones). I've got a bit more work to do,
> >>>but
> >>>when it's done this will "just work", in the future.
> >>>
> >>>John
> >>>
> >>>On Tue, Nov 22, 2005 at 02:03:52PM +0100, andrea spitaleri wrote:
> >>>
> >>>
> >>>
> >>>
> >>>>Hi all,
> >>>>I have a file.pdb with CONECT flag at the end giving the S-S connection
> >>>>atom numbers. While in pymol or insight I can see the S-S bond,
> >>>>in vmd it doesn't appear at all. I am wondering if it is a problem of
> >>>>cutoff since the dist is quite large (0.25nm).
> >>>>Any help??
> >>>>
> >>>>Regards,
> >>>>Andrea
> >>>>--
> >>>>-------------------------------
> >>>>Andrea Spitaleri
> >>>>Dulbecco Telethon Institute
> >>>>c/o DIBIT Scientific Institute
> >>>>Biomolecular NMR, 1B4
> >>>>Via Olgettina 58
> >>>>20132 Milano (Italy)
> >>>>Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
> >>>>-------------------------------
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>--
> >>-------------------------------
> >>Andrea Spitaleri
> >>Dulbecco Telethon Institute
> >>c/o DIBIT Scientific Institute
> >>Biomolecular NMR, 1B4
> >>Via Olgettina 58
> >>20132 Milano (Italy)
> >>Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
> >>-------------------------------
> >>
> >>
> >
> >
> >
>
> --
> -------------------------------
> Andrea Spitaleri
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
> ------------------------------- 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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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