Re: [ccp4bb]: Ligplot/Molscript/Breaking Bonds

[<deh22@cornell.edu>]

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This is probably a laborious solution, but instead of using something like:

ball-and-stick in residue 100;

You could not use the residue keyword and create the bonds individually 
for the residues in question:

bonds <atom-selection> <atom-selection>;

By doing this, you don't have to change the bonddistance parameter 
(probably).

Atom selection will definitely be complicated.  You may want to use 
something esoteric like "in not atom CA"...  The online manual has some 
better examples.

Darrell


On Thu, 6 Feb 2003 phubbard@post.its.mcw.edu wrote:

> Thanks for the reply. I had thought of that, but how do you change the
> setting within a residue, so as to keep some bonds formed and others
> broken?
> 
> > It should be possible to "break" the bonds by selecting the
> > appropriate atoms and setting the bonddistance parameter to something
> > really small (0.1?).  The selection rule may be somewhat complicated...
> >
> > Darrell Hurt
> >
> >
> > On Thu, 6 Feb 2003 phubbard@post.its.mcw.edu wrote:
> >
> >> ***  For details on how to be removed from this list visit the  ***
> >> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >>
> >> Hello all,
> >>
> >> Has anyone tried taking the flattened PDB from Ligplot and using it in
> >> Molscript? The highly distorted output I get means some atoms are
> >> close to eachother in the ligplot.pdb file, and so are bonded when
> >> they shouldn't be.
> >>
> >> Is it possible to "break" bonds in molscript? I've RTFM and still have
> >> NFI.
> >>
> >> Thanks
> >>
> >> AGS
> >>
> >>
> >>
> 
> 
> 
>