[phenixbb] on ligand restraint

Smith Liu smith_liu123 at 163.com
Sun Oct 4 21:51:28 PDT 2015

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.


At 2015-10-05 02:14:28, "Pavel Afonine" <pafonine at lbl.gov> wrote:
>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
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