Nathaniel
The atom names in the file I sent have the correct atom names as
defined by the PDB for ACD. Naturally, the atom names in your PDB file
and the restraints CIF file should match and given that you need the
correct names to deposit your structure into the PDB, then I would
recommend doing
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 wo
Nathaniel
I made a small mod to eLBOW (which will be available in the next
nightly build) that allows you to get an all cis ACD from a SMILES
string. I have attached the result. Note that the name of the file has
for the four cis (zusammen) configurations. As Paul suggested,
the torsion value
On 29/11/10 16:17, Nathaniel C. Gilbert wrote:
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 co
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.
