Subject: Qsar programs

From: Ojitos <[email-masked]>
Date: Wed, 11 Jun 1997 16:16:21 -0300 (ARST)

Hi.
  
I'm intersted in any a program that can make a regresion analisis of a
group of descriptors for a molecule and a set of analogues.

Does anyone know of a program for modeling drug receptor interaction with
semiempirical or ab initio methods?

        Thanks. 

Adrian Turjanski
[email-masked]

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From: Chris Harwell <[email-masked]>
Date: Wed, 11 Jun 1997 15:44:01 -0500 (CDT)

Thank you all for your responses to my animation query.  Responses 
(minus names) are attatched.  They have also been posted at

http://www.chem.lsu.edu/htdocs/people/crharwell/anim.htm

in the same form.

Chris Harwell    	        	 [email-masked]
http://www.chem.lsu.edu/htdocs/people/crharwell/index.html
Louisiana State University; 232 Choppin Hall F7; Baton Rouge LA 70803

"Everything positive originates in a positive attitude from someone" :>

Simple Animation Links for Atoms & Molecules

These are in responce to a CCL query for a program to animate pictures of
molecules and change color (to represent charge) during the process.
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   * Spartan http://www.wavefun.com
          This seems to be do-able in unix Spartan (supports AIX4.1) which
     is commercial. The molecular builders allow you to construct the
     molecules one by one, and then you group them together as a list. The
     list dialog has animation feature to scan through the list frame by
     frame. Color information can be altered by users.

   * Rasmol http://www.umass.edu/microbio/rasmol/
          Rasmol 2.6 has a minor fix (SET WRITE ON) that allows reading a
     series of atom coord files and writing corresponding .ppm files within
     a script; the .ppm files can be made into an MPEG animation using
     mpeg_encode. There does seem to be a limit on either the number of text
     lines in a script, or the number of coordinate files read, etc. within
     Rasmol. I've appended a partial example .

   * VMD http://www.ks.uiuc.edu/Research/vmd
          there is a program called VMD which is free, is supposed to do
     more than you want and as far as I know runs on a pc as long as you
     have OpenGL on it. But for what you want, is perfect.

     You can represent the molecules any way you want, you can render the
     image, you can animate it by loading multiple pdb files or a
     trajectory, you can ask the program to change any color you want for
     any atom you want during the animation and you can also take a snapshot
     of each frame. All these you can have set up in one script using Tcl or
     do you by hand.

     For a sample of the animations you can do with it check the web at the
     same location.

   * VMD http://www.ks.uiuc.edu/Research/vmd/
          can write to various 3D file formats, like POV-Ray{2,3}, Raster3D
     and VRML, as well as do trajectory animations and run in batch mode.
     VMD is free and runs best on SGIs, but slower version (because of the
     emulated OpenGL) are available for HPs and Linux.

     The biggest problem is that no one with a strong rendering background
     has worked on the code so there aren't really the hooks to tweak things
     that one might expect (eg, for making all the carbons be ebony or the
     surface be made of semi-transparent glass. We are open to suggestions,
     and you can get the VMD source to add your own tweaks.

     For a short tutorial I wrote a few months ago for making movies (with
     Raster3D), see http://www.ks.uiuc.edu/Research/vmd/workshop/movie.html
     (The general workshop notes, which help give an idea what VMD can do
     are at http://www.ks.uiuc.edu/Research/vmd/workshop/ .)

   * gOpenMol http://laaksonen.csc.fi/gopenmol/gopenmol.htmls

   *      Re_View
     http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm It sounds
     like Re_View(2) is exactly what you want. It provides complete control
     of atom colours, etc; enables multistructure XYZ files to be read in;
     displays animations and even drives POV-ray without the user having to
     know anything about the ray-tracing processes so that mpeg and AAplay
     movies are automatically generated.

     Best of all it runs under Window3.1/95/NT.

     PS: Re_View contains many more features including 'active' graphs of
     data, etc.

   * ICMlite (see http://molsoft.com ) can do 1,2,3. It is now free for
     academics. You can do something like this:

     for i=1,100

     read pdb "frm"+i # i.e. frm1.brk, frm2.brk etc.

     display xstick

     color a_//* Charge(a_//*)

     color background i # this is crazy, though

     delet a_

     endfor

   * http://www.povray.org
          For those of you interested in rendering high-quality movies, I
     can recommend PovRay, a highly sophisticated public domain renderer
     (there is a usenet newsgroup on it out there). I know there are several
     conversion filters, e.g. pdb->pov for itaround. In a Unix environment,
     one would most likely use pipes, or a batch soldering individual frames
     into a movie.

     The new version, povray3, has many improvements, including orthographic
     projection and several internal changes to increase rendering
     efficiency. If you tried PovRay over a year ago and thought that it was
     too slow for animation, I'd suggest trying it again. You can also use
     the features of PovRay to make animations based on a single coordinate
     set, e.g. rotations, pans and zooms, lighting changes, etc.

     A caveat about pdb2pov-- it creates one or two large compound objects
     using the constructive solid geometry (CSG) feature of PovRay; this
     defeats most of the new changes for efficiency, which in general apply
     divide-and-conquer approaches based on the number of objects and their
     distribution in space. Removing the CSG statements (e.g. merge or
     union) results in 50-fold decreases in rendering time for scenes with a
     few thousand atoms. I modified the copy of pdb2pov at our local site to
     avoid the use of CSG in the output .pov files. I've forwarded this
     information to the author of pdb2pov, who is working on a new version
     (as time allows).

     Like any programming language, it takes a little time to learn how to
     make the best use of PovRay. However, the documentation is available in
     HTML format and is very good for a public domain program. The results
     are also well worth the effort; PovRay has many pre-defined textures
     (e.g. glass, stone, wood, ...) and other features that can be used to
     produce journal-cover quality molecular images.

   * ChemSymphony http://www.cherwell.com/chemsymphony
          Animation is one of the features of ChemSymphony (URL below) which
     is a publishing tool for including structures in HTML documents. This
     essentially works by creating a series of frames which are rendered in
     series. It recognises most file formats (XYZ, XMOL, PDB and so on) and
     allows the net user to change orientation and manipulate the structure
     whilst the animation is going on. A free demo is available from the
     Cherwell web site.

     Check Out ChemSymphony - rated top 1% Java applet by JARS

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