VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 30 2005 - 10:15:45 CST

Hi,
  I believe that the newest versions of MSMS have dropped support for the
"all" option. VMD is the only program that ever used this feature of MSMS,
and it was never available throught the file-based MSMS interface apparently.
As such, I've been planning on removing the "all" control from VMD in the
short term. I could possibly emulate the behavior MSMS used to provide with
the "all" option by sending MSMS all atoms, and then removing all surface
elements that correspond to unselected atoms before the surface is
generated by VMD. If I went through the trouble of writing such code, it
could potentially be made to work for both MSMS and for Surf, and possibly
with the new VolMap tool or other surface data. If you really need to use
the "all" option in the short term, you'll need to use an older MSMS binary
to get that feature. Another way to do this would be to run MSMS manually
producing .vert and .face files and post-process them with a program/script
to do what I describe above, eliminated facets that correspond to atoms
that aren't selected. That's something you could do with a Tcl script if
you really want it badly enough. I don't think I'll have time to work on
implementing an emulation of the old MSMS "all" feature for a while yet,
but I hope this explanation helps you out in the mean time.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 30, 2005 at 11:10:05AM +1100, Eden Duthie wrote:
> Hi.
>
> I have been looking at a bug that occurs with the MSMS interface for
> various versions of MSMS and both the linux and macosx versions of VMD
> 1.8.3.
>
> The interface with MSMS correctly displays the total surface of a
> subselection of atoms. However the contribution of the subselection to the
> total surface of the molecule does not work. Here is the procedure that
> leads to the error:
>
> 1. load a pdb, eg 1PQ1.pdb
> 2. Go to Graphics->Representations and create a new representation with
> just part of the molecule e.g. residue 1 2 3.
> 3. Select the new representation and change the drawing method to MSMS.
> 4. The total surface for the selected representation is displayed correctly.
> 5. When the selection under "Which Atoms" is changed to All rather than
> Selected no surface is displayed. The aim is to display just the
> contribution of the selection to the total surface rather than the total
> surface of the selection.
>
> The error that is output on the console is:
>
> ERROR) No data from MSMS.. giving up.
>
> I was wondering if there is a known way round this problem. I have tried
> looking into the cause of the problem but I am unable to compile the
> source code on my system. Any hints on what is going on?
>
> Regards,
>
> Eden 

-- 
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