Re: [ccp4bb] restraints for cis-bonds, ACD cif file

[Nathaniel C. Gilbert]

I appreciate the input Paul and Nigel. The cif dictionary file you sent me 
doesn't have matching restraint definitions for 53 atoms in the ACD file. I 
opened the cif file you sent and extracted the SMILES code for ACD. Then I ran 
it in phenix.elbow to have it generate a pdb of the ACD. Then i would use the 
cif file you sent and import it into coot or phenix.refine, but it would not 
match the cif and pdb. I can wait for the new nightly build to come out, but I 
was wondering why this process wouldn't work.

Paul, I'm not as familiar with the CCP4 suite. Refmac5 doesn't give me as many 
new Fo-Fc peaks to build more model into as does phenix.refine even though 
Rfree numbers are comparable.

[ccp4bb] restraints for cis-bonds, ACD cif file

[Nathaniel C. Gilbert]

I have arachidonic acid soaked into my crystal structure and want to model it. 
The phenix.refine is allowing my cis double bonds to distort to a gauche or 
trans form. Is it the cif file or the refinement restraints in the program that 
I need to correct.