Q.034 - How do I get the same view in MOLSCRIPT as in O ?

Category: S.034 - plot

There's a little jiffy program in OMAC called GS2MOLSC (the source is file://rose.bmc.uu.se/pub/gerard/gs2molsc.f), written by Rams here in Uppsala.

You save your view matrix in O as follows: 

 O > write .gs_real nice_view.o ;

This file looks as follows: 

 .GS_REAL                  R         20 (8(x,f8.4))
   0.5535  21.8430   1.2260   4.0530   0.0209  -0.1431   0.1057   0.0000
   0.1761   0.0017  -0.0326   0.0000   0.0251   0.1077   0.1409   0.0000
  -0.7748   2.6863  -2.8390   1.0000

Then you run GS2MOLSC: 

 % 649 gerard rigel 22:39:08 pg/o > omac/GS2MOLSC
 Name of "O" gs_real file : nice_view.o
 Name of MOLSCRIPT include file : nice_view.molsc

The result is a small file which you must include in your MOLSCRIPT input file: 

           by rotation         0.02090
                               0.17610
                               0.02510
                              -0.14310
                               0.00170
                               0.10770
                               0.10570
                              -0.03260
                               0.14090  ;

Note added on 931202: Janet Smith has written a better program called O2MOL. Fortran source code and SGI executable are also in the OMAC directory. In O, do: 

 write .gs-real gsreal.odb (3f15.10)

then do: 

 omac/O2MOL < gsreal.odb

and cut and paste the output into your MolScript input file. Janet wrote:

"I have [uploaded] a program for converting the O display matrix into MolScript commands. It is called o2mol.f and should be compatible with any Fortran compiler.

o2mol takes a .gs_real datablock, extracts the scale factor, orthogonalizes the matrix (in a subroutine by Morten Kjelgaard), and produces three outputs:

  1. rotation command for MolScript using the orthogonalized matrix
  2. rotation command for MolScript using Eulerian angles
  3. .lsq_rt_gs datablock including both rotation and translation components.

This transformation, when applied to stored atomic coordinates, will produce new coordinates in Angstroms with the current screen center as the origin."