VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 28 2005 - 10:24:32 CDT

Hi,
  I compiled and tested your plugin on my machine here and I fixed
a few minor bugs in it. This new version should be compileable with
both the old VMD 1.8.3 versions and with the latest test version of
VMD 1.8.4. (I added ifdefs for the changes in the plugin interface for you)
I was able to load your example molecule and get atom colors etc.
Your original code wasn't assigning the atom name, and the atom type field
was overrunning a buffer, so that may have been what caused your crash.
Try the attached version of the plugin code and see if it works better
for you.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 28, 2005 at 09:55:51AM -0500, John Stone wrote:
>
> Hi,
> Once you've got the code compiled, copying it into your VMD
> installation directory will indeed work, but for the purposes of
> testing a new plugin, it's actually easier to load it interactively
> in the VMD text console:
> plugin dlopen /home/johns/plugins/compile/lib_LINUX/vmfplugin.so
> plugin update
>
> Assuming you've done everything correctly, after the 'plugin update'
> command, your plugin will be listed in the file loading menu of VMD.
> If VMD crashes when you load your plugin, that would indicate that you've
> got a bug in your code that's illegally accessing memory, or something
> similar. If it crashes immediately when the plugin is loaded, then you'll
> need to double check your VMDPLUGIN_register() routine and make sure
> it's correct. Let me know if you need help with this.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Fri, Oct 28, 2005 at 11:32:59AM +0800, baogen duan wrote:
> > Hi,
> > I want to VMD to read a new file type(*.vmf).
> > My steps are as follows:
> > (1)I downloaded Linux opengl,source code from the
> >
> > website.
> > (2)I wrote a plugin(vmfplugin.c) according to
> > mol2plugin.c. There are two directories in source
> > code. One is plugins,the other is vmd-1.8.3.
> > I copied vmfplugin.c to
> > ./../plugins/molfile_plugin/src
> > then cd to ../../plugins,typed 'make';'make LINUX'.
> > vmfplugin.so was created in ../../plugins/compile/
> > Lib_Linux/molfile.
> > (3)I copied vmfplugin.so to
> > ./../vmd-1.8.3.bin.Linux.opengl.tar.gz_FILES/vmd-1.8.3
> > /plugins/Linux/molfile.
> > (4)cd
> > to../../vmd-1.8.3.bin.Linux.opengl.tar.gz_FILES
> > /vmd-1.8.3,then'./configure',cd src 'make install'.
> > (5)When I operated File->New Molecule->determine
> > file
> > type->vmf->filename(*.vmf)->load.The interfaces of VMD
> > disapear at once.
> > My questions are as follows:
> > (1)Is this method feasible to embed a new file type
> > to
> > VMD?
> > (2)How does VMD recognize an atom's type(C_3,H_
> > etc.in
> > *.vmf) and a bond's type(S,D in *.vmf)?
> > (3)How is every atom linked?
> > (4)would you like to give me some advives about my
> > program(vmfplugin.c).
> > (5)What shall I do in order to embed a new file type
> > to
> > VMD except writing a plugin(vmfplugin.c)?
> > Attachments are vmfplugin.c and ch3oh.vmf.
> > Thanh you very much!
> >
> >
> >
> >
> >
> >
> >
> >
> > ___________________________________________________________
> > 雅虎免费G邮箱－中国第一绝无垃圾邮件骚扰超大邮箱
> > http://cn.mail.yahoo.com
>
> Content-Description: 3839761103-vmfplugin.C
>
>
>
> --
> 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 

-- 
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