[phenixbb] on ligand restraint

Pavel Afonine pafonine at lbl.gov
Sun Oct 4 23:12:39 PDT 2015


Most likely wrong ligand CIF file.
Pavel

On 10/4/15 21:51, Smith Liu wrote:
> Dear All,
>
> I have tried a phenix.real_space_refine with a ligand cif and without 
> ligand cif (both with ligand PDB in the whole protein-ligand PDB for 
> refine), I find with ligand cif in the input can lead to significant 
> increase of the clash score for the refined PDB.
>
> Will you please make comment on whether the clash score incensement by 
> adding cif in the input was a general phenomenon, or only specific to 
> my situation, and how to solve it?
>
> Best regards.
>
>
> Smith
>
>
>
>
>
> At 2015-10-05 02:14:28, "Pavel Afonine" <pafonine at lbl.gov> wrote:
> >Yes.
> >Pavel
> >
> >On 10/4/15 02:19, Smith Lee wrote:
> >> Dear All,
> >>
> >> Does phenix.refine can process some ligands without the process by eLBOW, for example ATP, ADP,etc?
> >>
> >>
> >> Smith
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >> Unsubscribe: phenixbb-leave at phenix-online.org
> >
> >_______________________________________________
> >phenixbb mailing list
> >phenixbb at phenix-online.org
> >http://phenix-online.org/mailman/listinfo/phenixbb
> >Unsubscribe: phenixbb-leave at phenix-online.org
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20151004/3e35eb5a/attachment-0001.htm>


More information about the phenixbb mailing list