[phenixbb] CUA Ligand issue

Jeff Headd jjheadd at lbl.gov
Thu Apr 7 09:25:54 PDT 2011

Hi Bradley,

I had a look at 1yew, and the issue is that the distance between the
CU1 and CU2 atoms in the three CUA het groups is a lot longer than the
expected distance defined in the chemical components dictionary, and
for some reason this causes elbow to choke.

Until we figure out exactly why it is crashing in this case, you can run:

phenix.elbow --chemical-component=CUA

This will generate a .cif file based on the chemical component
dictionary of CUA, and if you provide this .cif file to phenix.refine
it will progress as you expect.

After refinement, you should have a close look at these CUA het
groups, though, and see if the density supports the relative atom
positions as they are in the original PDB file, of if the dictionary
definition is more appropriate.


On Thu, Apr 7, 2011 at 6:53 AM, Bradley Hintze <bradley.hintze at duke.edu> wrote:
> Hello,
> I am trying to refine PDB 1YEW using the default phenix settings.
> $phenix.refine 1yew.pdb 1yew.mtz
> yields:
> '''
> Sorry: Fatal problems interpreting PDB file:
>   Number of atoms with unknown nonbonded energy type symbols: 6
>     Please edit the PDB file to resolve the problems and/or supply a
>     CIF file with matching restraint definitions, along with
>     apply_cif_modification and apply_cif_link parameter definitions
>     if necessary.
> '''
> $ phenix.ready_set 1YEW_H.pdb
> yields:
> '''
> Sorry:
>     Atoms in the input are supposed to be bound
>     CU1(CUA) - CU2(CUA) = 2.58
>     Fix the input file and retry
> '''
> I assume this means that the Cu atoms in CUA are at
> an inappropriate distance. Is there an easy way to find out what the
> appropriate distance is? Can I fix this in coot?
> Thanks,
> Bradley
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