From: John Stone (
Date: Fri Mar 12 2004 - 17:06:36 CST

  The clipping plane implementation is very new, and may be revised,
so the documentation only describes it in a minimalistic way.
Upcoming versions of VMD may implement it very differently,
so in reality its not a feature I'd expect more than 1% of users to
try at this point. That said, clipping planes are just that, planes,
so they have a point on the plane, and a normal that defines the plane
orientation. The status is simply on/off, there's not much more to say
about them other than to give examples of how one might want to use them,
given the very crude implementation that's currently available.

In any given version of VMD there are usually 5 or 10 new things that
are very preliminary implementations of new features which are subject to
further (sometimes radical) changes, and so those invididuals that want to
use them end up having to go through some of what you're going through now.
I don't want to encourage the masses to use partially-baked features, so
such features typically get very minimalistic documentation so that only
the die-hards are encouraged to use them. The other option would be for
me to not document these things at all until the "final" implementation is
complete. You can see that there are issues on both sides. I have to split
my time between answering VMD emails, writing code, writing documentation,
updating the web site, and numerous non-VMD things, so I have to be pretty
ruthless in gauging how much time to spend on documenting things that aren't
quite ready for prime time. You've just happened to choose one of them as
an example.


On Fri, Mar 12, 2004 at 03:49:28PM -0600, Jerry Ebalunode wrote:
> Hi John,
> Where in the documentation would you find the full decription and examples of
> how to use these clip comands? The link you sent just only stated the
> commands, no one new to vmd will know what they do and even how to get them
> working properly just by looking at the page you refered me to. For
> instance it took me thirty minutes to know that you need to use the " mol
> clipplane status .... " not to just get the status but to also activate
> clipping I just did. Probably the documentation needs a lot of improvment in
> support of this, one of the crystallographic postdocs in our dept. complained
> to me that the documatation is not straight forward or clear, when I
> introduced him to vmd. Now I see what he meant.
> This clip feature is such a wonderful feature for us decribing ligand binding
> in the easiet fashion possible but yet the documentation only spent 3 lines
> just stating commands and noting more not even what it means.
> On Friday 12 March 2004 10:11 am, John Stone wrote:
> > 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:
> > 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.
> >
> >
> > 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.
> --
> Cheers,
> Jerry Ebalunode
> Graduate Research Assistant
> RM 402F Houston Science Center
> Phone: 713-743-8367
> Dept. of Biology and Biochemistry
> University of Houston
> 4800 Calhoun Road
> Houston, TX 77204

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