[phenixbb] Restraints for small molecules in macromolecular crystal structures

Marie Elizabeth Fraser frasm at ucalgary.ca
Thu Jun 10 06:08:18 PDT 2021


The parameters we use as restraints for small molecules in complex with macromolecules have improved greatly, but we still get complaints when submitting to the Protein Data Bank. We use grade to obtain restraints for these small molecules, but when we submit to the PDB, some of their restraints do not match. I am not clear where the PDB gets these restraints, but we edit our file to match the values sent and finish the refinement.  What do others do?

As well, PHENIX and COOT aren’t accessing the same library for restraints. Is this due to how I’ve installed ccp4 (for COOT) and PHENIX?

The small molecule whose restraints I currently need is ADP metavanadate (AD9), which grade won’t accept because of the vanadium, so I used elbow to calculate restraints.

Thank you,   Marie

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