On Tuesday, January 24, 2012 09:53:55 am Paul Emsley wrote:
> Now that Coot uses the restraints dictionary to render ligands it has
> become apparent that the method of doing so is problematic for typical
> working situations.
>
> Say for example your read in
> complex-XYZ00123456.pdb in which the ligand is called LIG
> You read in the dictionary for XYZ00123456 and the ligand looks fine.
>
> Now read in
> complex-XYZ00123457.pdb in which the ligand is called LIG
> Different compound, same name, so same dictionary is used to render
> XYZ00123457.
> Result: tangled mess
>
> Read in dictionary for XYZ00123457 and now complex-XYZ00123457 looks
> fine but XYZ00123456 is a tangled mess because the restraints for LIG
> have been overwritten.
Heh. I've suffered from that problem more than once.
But it only takes minute to execute a "%s/LIG/FOO/" command in vi
and reload the files.
> So I am considering adding in a hack to Coot to make this situation less
> problematic.
>
> A potential hack is to specify that it is to be used for molecule number
> N (or a set of Ns) only.
Would it be easier to do it in the other direction?
For each model that requires a non-standard library, you would have
to register it first.
Similar to Extensions->Dock Sequence->Associate Sequence.
Ethan
>
> Doing this would make Coot internals messy so I have make this request
> for comments before I spend time reworking things and producing a
> solution that no-one will use.
>
> Thanks,
>
> Paul.
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
