VMD-L Mailing List

From: Dr. Daniel James White PhD (dan_at_chalkie.org.uk)
Date: Thu Apr 14 2005 - 09:17:40 CDT

Hi John,

I am trying to make movies of viral capsids.

So... I am using msms to make low resolution triangle surfaces,
so I dont run out of memory,
and I'm using the biological unit pdb file
1c8g.pdb1 which has 60 "states"

Problems:

1) On fedora core 3 linux,
I have downloaded and installed correctly msms 2.5.5. and vmd 1.8.3
msms works from the command line with command
msms
and alo I have pointed $MSMSSERVER to /usr/local/bin/msms
but VMD gives this error when I try to make an MSMS surface.

ERROR) Could not connect to MSMS server ...... etc. etc etc.

my /etc/hosts file contains

127.0.0.1 modeling.bio.jyu.fi modeling
localhost.localdomain localhost
127.0.0.1 localhost localhost

commenting out the top line still gives the same error.

same version of MSMS seems to work just fine with VMD 1.3.8 on my OSX
machine.

2) I was using VMD 1.8.3b on linux to do the
Graphical Reprsentations-trajectory-draw multiple frames
thing to show all sixty subunits of the virus.

today I updated it to 1.8.3
now on linux and OSX VMD 1.3.8 this no longer seems to work.

I type in
0:59
in the box as before,
and hit return,
but nothing happens.
In 1.8.3b doing this showed all the 60 molecules.

What am i doing wrong!?

cheers

Dan

Dr. Daniel James White BSc. (Hons.) PhD
Bioimaging Coordinator
Nanoscience Centre and
Department of Biological and Environmental science
Division of Molecular Recognition
Ambiotica C242
PO Box 35
University of Jyväskylä
Jyväskylä FIN 40014
Finland
+358 14 260 4183 (work)
+358 468102840 (mobile)

http://www.chalkie.org.uk
dan_at_chalkie.org.uk
white_at_cc.jyu.fi