[phenixbb] Hydrogens of ligands generated in elbow explode in coot realspace refinement

Paul Emsley paul.emsley at bioch.ox.ac.uk
Thu Dec 6 14:56:20 PST 2007

Schubert, Carsten [PRDUS] wrote:
> when I refine a ligand with hydrogens in coot using realspace 
> refinement, the hydrogens explode into the surrounding density. 

This is a known issue with Coot.

> This 
> only happens with ligand/cif files generated in elbow and not libcheck. 

Coot has had some tuning vs libcheck, but little vs elbow.

> Coot apparently needs and additional loop in the .cif file: 
> _chem_comp_tree.xxxx, which is missing from the elbow output.

Hmm... I wonder why you think so.  This may well be addressed in a more 
modern Coot.

> Unfortunately the geometry generated by libcheck is pretty dismal, so I 
> can probably get around this by running libcheck on the refined coords 
> from elbow ...

Urgh - non-optimal.

> Nigel, is it possible to fix elbow for the next rc?

I'm not sure that it is on Nigel's door that you should be banging. 
Maybe you, me and Nigel can get this sorted out (preferably testing with 
something non-proprietary).

>  coot 0.33 

0.4 will be out soon.  I'd recommend the upgrade.



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