[phenixbb] Refining sucrose

Nigel Moriarty nwmoriarty at lbl.gov
Mon May 23 07:30:06 PDT 2011


> How can I apply more stringent restraints to the ligand so its geometry wouldn't get so twisted?

You can tighten the ESDs of the restraints but I think you will find
that there is something else wrong with the refinement. Its possible
that sucrose is reversed or there is a lack of electron density.

> This might not be the most appropriate list for my second question, but the problem is the same and somebody probably knows: how to manually modify that sucrose in Coot (eg rotate only one ring or a -CH2OH group) or perform real space refinement? Right now I can only rotate/translate the whole sucrose and trying to perform a real space refinement results in an error ("Failed to match (to the dictionary) the following model atom names: SUC C1 C2 C3 C4 C5 C6 O1 O2 O3 O4 O6. That would cause exploding atoms, so the refinement didn't start.")
> I haven't specified any custom cif libraries as SUC should be present in the built-in library of both Phenix and Coot. I'm using Phenix v1.7.1-743 and Coot v0.6.2-pre-1-rev3450 on OS X 10.6.7.

PHENIX is using the standard SUC restraints from the Monomer library.
I don't know about COOT but you are able to load the restraints from
PHENIX into COOT. To find the PHENIX library use

elbow.where_is_that_cif_file SUC


Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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