VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 12 2004 - 10:11:26 CST

Jerry,
  At present the only way to compute and display MSMS surfaces in VMD
is via the socket connection mechanism you asked about, there's no alternative
way at present. Most people that encounter problems with MSMS are missing
"localhost" in their /etc/hosts file, be sure you have it in there, it
should look like this:
127.0.0.1 localhost

If you have your machine locked down to the degree that apps running
on the same machine can't bind/open ports in the > 1024 range, this is
an abnormal unix configuration and its bound to cause problems for any
program that uses sockets, not just MSMS, so I'd recommend that you
consider setting up your machine in a more normal way. If VMD fails
to contact MSMS on port 1357, it will make attempts to open other ports
in an ascending sequence, apparently your machines are blocking all local
ports, so that's why it continues to fail.

Regarding your clipping question, yes, at present each representation
can be clipped individually.
  http://www.ks.uiuc.edu/Research/vmd/current/ug/node123.html#6936

The released version of VMD has a sign bug in the clipping plane
code that places the plane at the wrong center, you'll have to negate
your "center" to get it to show up in the right location if its not
at the origin.

  John

On Fri, Mar 12, 2004 at 08:11:43AM -0500, Jerry Ebalunode wrote:
>
> Hi John,
> Currently VMD runs the MSMS calculation using the socketPort option. So if
> the system is properly set to allow any user or program to open this port
> (in the case of VMD port No. 1357) then your calculation would proceed
> successfully and you can enjoy the fruit of Dr. Sanners work. However if
> your system ports are not set to allow usage by MSMS, you cannot
> render the MSMS surface. I have experienced this problems with two linux
> machines that I set up to use DHCP for getting there ip addresses. The
> first one I fixed by opening port manually using firestarter (an iptables
> firewall generation gui application). For the second one I couldn't
> get away with this trick. The next possible route is to set the machine to
> use a static IP address, since all linux machines that have static IP
> addrs., which I have installed vmd and msms runs msms calculation via vmd
> calls without any problems.
> Berore I do that, I have the following question regarding this issue"
>
> Can you set vmd to run msms without using the socketport option? If yes,
> how can this be done?
>
> Can do know of any other method to make port 1357 available for msms?
>
> Though this last question is not related, is it possible to incorporate
> the ability to clip seperate objects (i.e., you rendered a molecular
> surface of your protein in one representation and renderd a certain
> residues in cpk or licorice, however you want to just clip only the
> surface to a certain extent such that all the residues you are displaying
> as well as the rest of the surface could be seen simultaneously) into vmd
> design. Probably someone already asked about adding feature this before,
> but I need to let the VMD developing team what my additional needs are.
> Thanks for you reply in advance.
>
> Cheers,
>
> Jerry Ebalunode
> Graduate Research Assistant
> Dept. Biology and Biochemistry
> University of Houston
> Houston, Texas.
> 

-- 
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