VMD-L Mailing List

From: Eden Duthie (eduthie_at_wehi.edu.au)
Date: Tue Nov 29 2005 - 18:10:05 CST

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