[phenixbb] Exploded ligands and phenix...
chern at ualberta.ca
Tue Apr 28 13:54:16 PDT 2009
are you sure that it's a phenix problem? Did you try other programs to
see your ligand after refinement?
I have seen a similar problem in coot with DNA. Coot would break up a
DNA when we tried to regularize it, due to a different letter code
convention for nucleotides. But when we changed A to Ad, G to Gd etc,
there were no problems.
Ruben Van der Meeren wrote:
> Hi Ralf,
> The coordinates of the ligand in the file I use for refinement are
> similar to those I posted. I uploaded an overlay of the original
> ligand and the ligand in my model. Green is model, blue is original...
> You can see the picture on this site:
> The cryst1 card of the pdb is the next:
> CRYST1 98.500 104.050 415.200 90.00 90.00 90.00 P 21 21 21
> The structure has 4 monomers in which I modeled a ligand monomer A and
> B. I also checked the .geo file. In most cases (for bonds and Angles)
> the model is almost equal to the ideal. For dihedrals there is much
> more disagreement. E.g. for one dihedral the model is 168° whereas the
> ideal is -60°. For non-bound interactions the distance is sometimes
> less than the VDW-radius. Could this be the problem? But this is in
> fact the thing I want to refine.
> The log file can be downloaded here:
> Citeren "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>:
>> Hi Ruben,
>>> I'm using phenix for the refinement of my protein (phenix.refine). But
>>> there is a problem...
>> Your pdb and cif file seem OK after a quick check (phenix.pdbtools
>> --geometry-regularization tre.pdb tre.cif).
>> My best guess is that the ligand conincides with a symmetry operation.
>> Are the coordinates in the pdb file you posted similar to the coordinates
>> in the file you used for refinement?
>> Could you send me the CRYST1 card?
>> The phenix.refine log would also be helpful.
>> Note that all geometry restraints are listed in the .geo file written
>> by phenix.refine. Look for nonbonded interactions involving your ligand.
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