From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 15 2009 - 11:38:22 CST

Cesar,
  It isn't so much an issue of the plugin, but rather of the plugin
interface, as there's not (presently) a way to give the jsplugin the
contents of the user fields. This is what I was alluding to in respect
to revising the plugin to eventually support this. In the short term,
writing a script to make a binary dump of the user fields would likely
be the easiest thing to accomplish.

Cheers,
  John

On Thu, Jan 15, 2009 at 04:33:09PM -0200, Cesar Luis Avila wrote:
> John,
> thanks for your reply. Is this "js" format implemented on the alpha test
> version? Perhaps the most simple thing for me to do is to play a little
> bit with the sources and implement my own "ca" format in order to
> load/save the data I want based on your "js" format. Which are the files
> that I should be looking for in order to modify?
> If the above is too difficult, I could also try to write the binary file
> with tcl. Do you have any scripting examples on how to do this? Just for
> orientation.
>
> Best Regards
> Cesar
>
> John Stone escribió:
> >Cesar,
> > You can download test versions of the next version of VMD
> >by following the instructions here:
> > http://www.ks.uiuc.edu/Research/vmd/alpha/
> >
> >The new test versions support multiple per-atom/per-timestep
> >user fields, so you can store things in "user", "user2", ..., "user4".
> >
> >The DCD format doesn't have any provision for storing anything other
> >than coordinates or unit cell data. I haven't added support for
> >loading/saving the user fields in the new "js" format, but that
> >might be a possibility. You could also do a bit of scripting and either
> >write a binary file containing frames of user data yourself (Tcl has
> >ways of doing this efficiently) or you could write a text file, all
> >by scripting. I'll see about adding support for the "user" fields
> >in a future rev of the "jsplugin".
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Wed, Jan 14, 2009 at 07:02:25PM -0200, Cesar Luis Avila wrote:
> >
> >>Dear all,
> >>Regarding what I found on a previous message from Axel Kohlmeyer
> >>
> >>
> >>>data fields like mass, charge, beta, occupancy are stored
> >>>once per molecule. the only data fields that are once per
> >>>time step are x, y, z, and user. only the latest alpha test
> >>>versions add to this (e.g. multiple user files and velocities).
> >>>
> >>I would like to know
> >>
> >>1- Which is the alpha test version that he is referring to?
> >>2- I think that also ufx, ufy and ufz are stored once per time step. Is
> >>there any problem on using these?
> >>3- It would be very nice to be able to save this data in a file in such
> >>a way that it could be easily restored and loaded along with the dcd
> >>file. Is there such a feature in vmd?
> >>
> >>Best regards
> >>Cesar Avila
> >>
> >
> >

-- 
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
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