[phenixbb] phenix.elbow: Best ploy to generate restraints files for similar compounds ?

Phil Jeffrey pjeffrey at princeton.edu
Thu Apr 25 13:01:09 PDT 2013

I've got homologues of small molecule compounds I want to generate 
restraints for.  The changes I'm looking at are converting O to S and 
moving a substituent around on a phenyl ring.  I expect them to have 
similar conformations overall.

Is the best method to:

1.  create a new PDB file of the homolog, change atom types and do some 
primitive modeling, assuming that the --opt method will fix geometry snafus


2.  use a SMILES string, edit the numbering of the PDB file and 
regenerate the restraints from that

Phil Jeffrey

More information about the phenixbb mailing list