[phenixbb] Real space refinment keeps messing up my taxol conformation

Ahmad Khalifa underoath006 at gmail.com
Sat Jul 20 15:17:32 PDT 2019

I'm still having issues with taxol ligand (TA1), check out attached
screenshot, despite using different methods (readyset, elbow,...etc) to
generate the restraints and upgrading from v1.14 to v1.16.

I would appreciate your prompt feedback with this!

On Mon, Jul 15, 2019 at 1:00 PM Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Ahmad,
> > I used elbow to generate restraints for taxol using chemical
> > componenet and sdf file. I posted before to the list and Oleg was kind
> > enough to provide restraints generated by readyset. No matter what
> > restraints I use, the taxol is messed up!
> >
> > The other thing is, the refinement keeps breaking the peptide bond at
> > a specific location! I would like to send some files to someone
> > privately to investigate!
> please send me files that show the issue:
> - model before and after refinement, and tell what residue number in
> what chain I need to look at;
> - map file and ligand CIF.
> Pavel
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