[phenixbb] Several problems with sugar refinement

Joe Krahn krahn at niehs.nih.gov
Thu Mar 3 07:34:38 PST 2011

I am working with sugar polymers and have run into several problems.

First, is anyone working on improving the handling of sugars?

ReadySet is getting most of the chiral restraints wrong for the sugars 
that don't already have parameters. It appears to convert all sugars to 
a standard chair conformation. For example, residue IDS gets 3 of 5 
chiral centers inverted, even when starting from an ideal-geometry PDB 
file containing all hydrogens. It seems like a serious flaw for 
automated ligand parameterization to make such an obvious error.

Another problem is that it is difficult to get the polymer links 
working, because many sugars don't have the same hydrogen nomenclature. 
Until that changes, we need better handling of the current residues. In 
most cases, only the hydrogen names are mismatched, so it would be great 
if PHENIX could ignore hydrogen atom errors in the case where hydrogens 
will not be used in refinement.

Can I give PHENIX "data_link_list" CIF data just for some residues, or 
will it have to contain the entire existing list?

Another problem is with LINK records. I tried to work around the polymer 
link problems by simply supplying LINK records. Unfortunately, LINK 
record processing requires REMARK 290 symmetry data, even if all entries 
have the identity symmop "1555". That is an unnecessary nuisance, 
especially since almost all LINK records have 1555. I discovered that 
leaving the symmop field blank works without REMARK 290, but why not 
make "1555" behave the same way. Additionally, how is the bond sigma 
derived? Does the link distance value have any effect?

Joe Krahn

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