VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 19 2006 - 17:46:14 CDT

Hi,
  The contact map plugin calculates distances between "CA" atoms,
so if you have differing atom names etc, it's not going to work.
You can use the "measure contacts" command to do the same type of
thing, but more efficiently and with no limitation on what atoms
you're able to compare. See the VMD User's Guide for more information
on that command.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 19, 2006 at 12:37:23PM +0200, andrea spitaleri wrote:
> Hi all,
> the contact map plugin under analysis menu may analyze the contact between
> ligand and protein?
> In first instance, it doesn't. Any t&t?
> Thanks
>
> Regards
>
> Andrea
>
> Marc Petitmermet wrote:
> >
> >On 18. Apr 2006, at 13:13 Uhr, Marc Petitmermet wrote:
> >
> >>I have this strange error upon starting vmd 1.8.4 (or 1.8.4b11) and
> >>fully patched Fedora Core 5:
> >>
> >> Tk startup error: this isn't a Tk applicationunkown color name "Black"
> >> Could not read the vmd initialization file -
> >> source {/usr/local/lib/vmd/scripts/vmd/vmdinit.tcl}
> >> can't invoke "wm" command: application has been destroyed
> >> The VMDDIR environment variable is set by the startup
> >> script and should point to the top of the VMD hierarchy.
> >> VMD will continue with limited functionality.
> >> invlid command name "vmd_load_extension_packages"
> >>
> >>I did not have this problem with test 3 of Fedora Core 5 and the
> >>vmd-1.8.4b11. Something must have been changed. I used the standard
> >>installation procedures (unpack; ./configure; cd src; make install);
> >>vmd files from earlier installations, if any, were removed before the
> >>installation. FC5 contains tk-8.4.12-1.2 and tcl-8.4.12.-4.
> >>
> >>When starting /usr/local/lib/vmd/vmd_LINUX I get first the error:
> >>
> >> Tcl startup error: Can't find a usable init.tcl in the following
> >>directories:
> >> (here comed a list of directories that do not exist in FC5)
> >>
> >>and then the same error message as mentioned before.
> >>
> >>How can I fix this problem? Am I missing something in my installation?
> >
> >
> >
> >Ok. My mistake. Had a nonexistent RgbPath setting in xorg.conf. Just
> >removed it and the problems are gone.
> >
> >Regards,
> >Marc
> >
> >
> >
>
> --
> -------------------------------
> Andrea Spitaleri
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> -------------------------------
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078