[phenixbb] Refining sucrose
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
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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