VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 03 2008 - 00:13:12 CDT

Ben,
  Regarding CVS, your best bet is to try getting to our CVS server
from a machine that's not blocked by whatever firewall you're being
affected by, or to ask your local security administration people to
open the CVS port 2401 so that you can access the server without problems.
There are a lot of new source files in the current CVS tree that
didn't exist when VMD 1.8.6 was released, this is a natural result of
ongoing development. The only solution I can recommend is to get your
network access issue resolved so that you can access our CVS server
without trouble. Many other people are using our CVS server without
problems, so I'm convinced you're being blocked by some sort of local or
campus level network firewall of some kind.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 02, 2008 at 09:26:36AM +0800, Ben Chern wrote:
> Hello, Axel,
>
> I'm not sure whether some plugin can do that.
> What I want to do is to show the bond energy between atoms.
> I think it should can be done using scripts.
>
> But as the VMD is opensource, and it uses OpenGL and integrates with other
> plugins, I am a freshman in OpenGL, so I want to follow the source code to
> learn some programming skills.That's the reason why I prefer to compiling
> the source code.
> I am reading the programmer's guide on the web, I've found there are some
> files, e.g. MeasureSurface.C, not included in the distributed source code,
> so I think I've to use the CVS to retrieve the latest source code.But as my
> last email said, I couldn't connect to the CVS server.
>
> On Tue, Apr 1, 2008 at 7:06 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> wrote:
>
> > On Tue, 1 Apr 2008, Ben Chern wrote:
> >
> > BC> Axel,
> > BC> Thanks for you advice.
> > BC> I'll try to compile the source under linux.
> >
> > ben,
> >
> > you still have not satisfied my curiosity!
> > what are you planning to change, once you
> > get VMD compiled? i am very curious to learn
> > what it is you have in mind, that cannot be
> > done in scripting, perhaps with the help of
> > a little plugin...
> >
> > cheers,
> > axel.
> >
> >
> >
> > BC>
> > BC> On Tue, Apr 1, 2008 at 10:47 AM, Axel Kohlmeyer <
> > akohlmey_at_cmm.chem.upenn.edu>
> > BC> wrote:
> > BC>
> > BC> > On Tue, 1 Apr 2008, Ben Chern wrote:
> > BC> >
> > BC> > BC> I want to show some chemical properties, e.g. bond energy, but I
> > would
> > BC> > not
> > BC> > BC> wish to do that using script.
> > BC> >
> > BC> > ben,
> > BC> >
> > BC> > "stupid question(TM)":
> > BC> > how do you plan to get those properties "into" VMD?
> > BC> > and how do you plan to visualize them, i.e. how are
> > BC> > they supposed to look like?
> > BC> >
> > BC> > before starting on a long and painful process where
> > BC> > you may at the end find out, that you won't get what
> > BC> > you planned, it may actually be a very good idea to
> > BC> > prototype what you want to do in scripting.
> > BC> >
> > BC> > this is how many of the features in VMD started (and
> > BC> > quite a few still are).
> > BC> >
> > BC> > BC> I have tried the CVS, but the error still exists.
> > BC> > BC> Would you please send me a tar file of the Windows build area
> > for VMD?
> > BC> >
> > BC> > also, have you considered using a linux/unix machine
> > BC> > for development? it is infinitely more convenient, the
> > BC> > way VMD "wants" to be built.
> > BC> >
> > BC> > just a few (curious) thoughts,
> > BC> >
> > BC> >
> > BC> > axel.
> > BC> >
> > BC> >
> > BC> > BC> Thank you very much.
> > BC> > BC>
> > BC> >
> > BC> > --
> > BC> >
> > =======================================================================
> > BC> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> > http://www.cmm.upenn.edu
> > BC> > Center for Molecular Modeling -- University of Pennsylvania
> > BC> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> > 19104-6323
> > BC> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> > 1-215-898-5425
> > BC> >
> > =======================================================================
> > BC> > If you make something idiot-proof, the universe creates a better
> > idiot.
> > BC> >
> > BC>
> > BC>
> > BC>
> > BC>
> >
> > --
> > =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
> >
>
>
>
> --
> Ben 

-- 
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