Help with Molscript bonds command

Joachim Meyer meyer at bio5.chemie.uni-freiburg.de
Thu Dec 21 04:13:39 EST 1995


In article <4b9jgi$1l2q at columba.udac.uu.se>, Bjorn Kauppi <kauppi at xray.bmc.uu.se> writes:
|> 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
|> ---------------------------------
|> 
|> 
|> -- Bjorn Kauppi

Dear Bjorn,

I prefer using the line command for hydrogen bonds:

set linecolour cyan;
set linedash  3.0; 	! if you want hydrogen bonds as dashed lines
set linewidth 1.6;

line position require atom  O   and in residue 883 to
     position require atom  O   and in residue 884;

Bye, Joachim

*****************************************************************
* Joachim Meyer	 	meyer at bio5.chemie.uni-freiburg.de	*
*			FAX: +49/761/5987			*
*	Abt. Prof. G.E.Schulz					*
*	Institut f"ur Organische Chemie und Biochemie		*
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