[phenixbb] phenix/ccp4 monomer library compatibility

Paul Emsley paul.emsley at bioch.ox.ac.uk
Tue Sep 4 04:55:57 PDT 2012

On 04/09/12 12:34, Wulf Blankenfeldt wrote:
> this may have been asked a thousand times, but: are the ccp4 standard 
> monomer libraries incompatible with phenix.refine, and if yes, is 
> there an easy way to resolve this?
> I am refining a structure with an FMN, which I build with the "get 
> monomer" option in coot. Unfortunately, phenix.refine doesn't like it 
> and throws it out. Using a cif generated with elbow, on the other 
> hand, has chirality errors (which I can fix...) and isn't liked by 
> coot (0.6.2), which refuses to refine the ligand.


Hi Wulf,

It seem that somehow you have an inconsistency between the model and the 

The correct atom names are defined by the PDB. e.g.


When I use "Get Monomer" I get a FMN monomer this is consistent with 
this (well, except for phosphate hydrogens). In particular, there are 
primed atom names (not starred).  If you are using - or referencing an 
old CCP4 distribution you may be picking up an old dictionary when using 
"Get Monomer" - coot should tell you in the console (at least) the file 
names that it reads.  If you want to reference the Phenix copy of the 
monomer library, you can use use COOT_REFMAC_LIB_DIR to point to it.

If you use the model (pdb file) and dictionary cif from elbow (and call 
it FMN) then coot should be happy no matter what the PDB says. And I 
would imagine that that would be so for phenix.refine also.


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