Subject: Phi-Psi plots

From: [email-masked] (Jeffrey L. Nauss)
Date: Mon, 11 Sep 1995 16:43:47 -0400

How do *you* handle phi-psi plots?  
 
We are working with some carbohydrate models and want to show contour
maps for rotation about the glycosidic linkages.  We also want to find
the most favorable combination of phi/psi between two residues.  (The
specific residues involve are unusual sugars.  So no one has made a
study like this before.)
 
The data is generated using Biosym's Discover using the rotors
command.  The output is a formatted *.tor file.
 
I can get a reasonable plot using Biosym's InsightII with Analysis.
Eventually, we would want to show the contours for publication
illustrations.  However, the plots from Analysis are truncated, i.e.
the axes are shorter than -180 to +180 degrees.  I am unable to expand
the axes to the the range.  Any suggestions on how to expand them?
 
Also, the Biosym plot does not leave a lot of flexibility for drawing
contours and labeling them for publication purposes.  
 
So what do others use?  Would GNU-Plot be useful here?
 
I'll summarize if I get any responses.

                                                Jeff Nauss
 
****************************************************************************
*  UU    UU             Jeffrey L. Nauss, PhD                              *
*  UU    UU             Director, Molecular Modeling Services              *
*  UU    UU             Department of Chemistry                            *
*  UU    UU CCCCCCC     University of Cincinnati                           *
*   UU  UU CCCCCCCC     Cincinnati, OH 45221-0172                          *
*    UUUU CC                                                               *
*         CC            Telephone: 513-556-0148    Fax: 513-556-9239       *
*         CC                                                               *
*          CCCCCCCC     e-mail: [email-masked]                    *
*           CCCCCCC     http://www.che.uc.edu/~nauss                       *
****************************************************************************

---

From: [email-masked] (Harry C. Johnson)
Date: Mon, 11 Sep 95 14:49:53 -0700

>>>>> "Jeffrey" == Jeffrey L Nauss <[email-masked]> writes:

    Jeffrey> How do *you* handle phi-psi plots?
 
I wrote a small utility program to go along with Spartan.  The program
will generate a 2 or 3 dimensional gnuplot data file from the list of
Spartan molecules resulting from conformational analysis (or reaction
coordinate) calculations.  This can then be used within gnuplot to
generate a Phi plot, or a Phi-Psi plot using contours, meshes, etc.

Feel free to drop me a note if you need more info.
-Harry

+-----------------------+------------------+-------------------------+
|Harry C. Johnson IV    |  ______________  | E-Mail: [email-masked] |
|Computational Chemist  |  \  _________	/  | Phone:  (714)955-2120   |
|Wavefunction Inc.      |   \ \\\\\\\\/	   | Fax:    (714)955-2118   |
|18401 Von Karman       |    \ \\\\\/	   |                         |
|Suite 370              |     \	\\/        | "Seems to me its all    |
|Irvine, CA 92715       |      \/	   |  just chemistry" - RUSH |
+-----------------------+------------------+-------------------------+