Help with Molscript bonds command

Bjorn Kauppi kauppi at xray.bmc.uu.se
Wed Dec 20 13:09:22 EST 1995


Hi,
I can't get the bonds command working in Molscript v1.4. I have tried all
(well) possible ways according to the manual. I have even tried the line
command without success. Can anyone please describe a working example.
I think I have missed something basic about Molscript syntax. It compiles
without any error messages but no bonds, se example below.

I want to display hydrogen bonds and metal ligand bonds in a nice Molscript
picture.

This is an example input:
--------------------------------
 plot
slab 20.;
 ! window 6;
  read mol "junk.pdb";
  transform atom *
    by centre position atom *;

ball-and-stick in residue 883;
ball-and-stick in residue 884;
set bonddistance 10.0, linewidth  3., linecolour red, depthcue 0.3;
bonds atom O2;

end_plot
----------------------------------
The junk.pdb file looks like this:
ATOM   2424  O2  HOH   883      86.624  79.143  67.180  1.00 45.96   8
ATOM   2425  O1  HOH   884      86.618  77.378  68.457  1.00 47.83   8
END
---------------------------------
And Molscript says:

alpha3 33% molscript < junk.in > j.ps
 MolScript v1.4 (C) 1993 Per Kraulis
 email: pjk at ciclid.csb.ki.se
 ref: P J Kraulis, J Appl Cryst (1991) 24, 946-950.
 reading PDB file...
 2 residues and 2 atoms read into molecule mol
 2 atoms selected for position
 2 atoms selected for transform
 rotation matrix applied:
 1.000000 0.000000 0.000000
 0.000000 1.000000 0.000000
 0.000000 0.000000 1.000000
 translation vector applied:
 -86.621002 -78.260498 -67.818497
 1 atoms selected for ball-and-stick
 1 atoms selected for ball-and-stick
 1 atoms selected for bonds
 setting window to 6.03
 writing graphical segments to PostScript output...
 0 lines, 2 spheres, 0 planes, 0 sticks and 0 labels written

-- Bjorn Kauppi
===========================================================================
 Swedish University of Agricultural Sciences
 Department of Molecular Biology, Uppsala, Sweden
 Voice phone:   +46 18 174550
 Fax:           +46 18 536971
 Internet:      kauppi at xray.bmc.uu.se
 WWW:		http://onyx.bmc.uu.se/~kauppi/
===========================================================================





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