From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 21 2003 - 15:36:56 CST

Dear Josh,
  Unfortunately the individuals that contributed the aligntool,
timeline, and contactmap extensions did not provide us with any
written documentation to accompany the plugins by the time we released
VMD 1.8. I can provide several comments on each however, since I've
used them before and helped the developers make them work with VMD.
If docs are yet forthcoming on any of these plugins, they'll be posted
immediately as soon as I have them.

Here's what I can tell you about each of those tools based on my
own experience helping people write them:

Aligntool
---------
  This tool provides a means to align two proteins using Phil Bourne's
Combinatorial Extension "CE" program:
  http://cl.sdsc.edu/ce.html
The aligntool scripts expect that you have CE compiled and installed on
your computer system, and that the cealign package (part of the aligntool
code) can find it and execute it. The authors of the aligntool extension
are Michael Januszyk and Zan Schulten. If you have questions about it,
perhaps the best thing to do is to email them directly:
  zan_at_uiuc.edu
  mjanuszy_at_uiuc.edu

Contactmap
----------
  This tool shows you the residue-residue distances for two molecules
as a 2-D map. Select the MoleculeA from the list, then MoleculeB, then
click on "Fit all" (to start out with) and select the menu item
Calculate->Res Res Distances, and you should get a color coded map indicating
the relative distances between the residues in a 2-D matrix form.
You can then change the scaling on the Y axis, scroll, etc.
Barry Isralewitz wrote this extension, you can email him at barryi_at_ks.uiuc.edu

Timeline
--------
Timeline is very similar to the regular sequence viewer except that it
plots one of several values from the Calculate menu, and displays them
over all residues, for each timestep in an MD trajectory. If you make a
selection in the 2-D map area, you'll see it highlighted on the 3-D structure
much like you would see with the sequence viewer. By selecting a 2-D
region of the map while holding down the shift-key, VMD will highlight
the appropriate region of the structure while animating the trajectory in
a loop over the selected range of timesteps 3 times in a row. You can
make various calculations and appearance settings by selecting items from
the menus, so this extension is somewhat more self-explanatory than the
others. Barry Isralewitz wrote this extension, you can email him at
barryi_at_ks.uiuc.edu

If you have other questions about VMD please let us know, I didn't write
these extensions so this is about the best seat-of-the-pants documentation
I can provide for you until the authors send me something better.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 21, 2003 at 04:03:36PM -0500, Joshua Speidel wrote:
> Hello,
>
> I'm looking for information on how to use the 'aligntool' in the Extensions
> dropdown list of VMD 1.8.. I'm trying to structurally align 4 different
> proteins that have some sequence homology. 'aligntool' sounds like it will
> do the trick, but I can't find any documentation on it on the VMD web page
> so I don't know how to use it or what it would do if I could get it to
> work.. :) Any help would be greatly appreciated.
>
> Thanks,
>
> Josh
>
> ps. if you can tell me where the documentations for Extensions|contactmap
> and Extensions|timeline are, I would appreciate it. Thanks! -j

-- 
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