VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Wed Sep 22 2004 - 14:23:04 CDT

If what you mean by superimpose is to align all the frames in reference
to another frame or to antoher structure you can try the rmsdtt plugin:
http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/index.html

Best,

Luis
John Stone said the following on 09/22/04 12:15:
> Amarda,
> What you've been told is inaccurate. You can use the
> "draw multiple frames" feature on the Trajectory tab of the
> graphical representations window to superimpose multiple trajectory
> frames on top of each other simultaneously. This does not require
> writing any PDB files or doing anything special other than specifying
> to VMD what frame range to draw etc. Since you didn't specify what
> file format these frames originate from, I don't know any details
> about your structure(s), but I'm assuming from your brief query that
> you're trying to visualize multiple trajectory timesteps at the same
> time, which is precisely what the 'draw multiple frames' feature is for.
> If you are running a version of VMD prior to VMD 1.8.2, you'll need to
> get VMD 1.8.2 in order to use this feature.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Sep 22, 2004 at 10:51:57AM -0500, Amarda Shehu wrote:
>
>>Hi all,
>>
>>I have been told that the only way to superimpose frames in vmd is to
>>write pdb files for each of them and then load these pdb files.
>>This is not possible when I have about 100 frames that I would rather see
>>superimposed on one another.
>>
>>I have been looking for scripts or anything that automatically does this.
>>If you have any pointers from experience, please let me know. I am trying
>>to make some pictures, so an animation won't cut it.
>>
>>-Amarda Shehu
>> Graduate Student,
>> Rice University.