[phenixbb] Exploded ligands and phenix...

Maia Cherney chern at ualberta.ca
Tue Apr 28 13:54:16 PDT 2009

Hi Ruben

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:
> http://gallery.me.com/ruben.vandermeeren/100216
> 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:
> files.me.com/ruben.vandermeeren/9tuifv
> Ruben
> 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.
>> Ralf
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