[phenixbb] Ligand CIF file in real space refinement

Nigel Moriarty nwmoriarty at lbl.gov
Mon Dec 6 12:07:49 PST 2021


It seems your request relies on the perception that restraints are not
allowed to exceed a certain point. It is much more complicated than a hard
limit as it's an optimisation that involves the EM data, the ideal
restraints values, the ESD values of said restraints and even the starting
geometry of the ligand. Have you validated the final geometry with
something like Mogul?



Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
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
ORCID : orcid.org/0000-0001-8857-9464

On Mon, Dec 6, 2021 at 2:01 AM Fadini, Alisia <
alisia.fadini15 at imperial.ac.uk> wrote:

> Hello,
> I am trying to use phenix.real_space_refine to improve the fit between my
> protein's ligand and the electron density.
> I include a CIF file that has worked well for reciprocal space refinement,
> made through JLigand.
> It seems to me that the CIF file is read properly, it does not produce
> errors and the restrains are stated correctly in the output .cif file that
> includes all protein + ligand atoms. However, the output pdb shows a
> distorted ligand, where specific bond angles and bond lengths have been
> modified past what should be allowed by the restrains.
> Any insights on how to improve/the causes of this effect would be very
> welcome!
> My command is : *phenix.real_space_refine model.pdb map.ccp4 ligand.cif
> resolution=1.63*
> *​*Thank you,
> Alisia
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