My cif file was for ATP, which was rather easily got by eLBOW as for the Phenix contains it in its library. Attached is the ATP.cif file I used.
In addition, I have run another 10 cycles of simulated_annealing+minimization_global, and the clash score was still 120 (too high).
Recently I fond for both the 1.9-1692 and 1.10.2155 version of phenix.real_spacea_refine, I got rather high clash score (higher than 20). In addition I found (recently?) the phenix.real_space_refine output PDB clash score was different from the Ramachandran clash score value. Is an possibility my Windows versions of phenix have something wrong?
I am looking forward to getting your further comment.
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@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
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