Dear Pavel,


I find some reasons for the high clash. If the protein part PDB is without H and the ATP PDB part has H, the final clash score will be high. But it seems cif does not permit ligand without H, am I right? If I add H to both the protein and ligand, the poor resolution (poorer than 4) may be does not like to have the H added. What is your opinion?

Will you please explain whether the phenix.real_space_refined pdb's clashing score is same with that of MolProbity? If same, then there may be something wrong with my phenix software, as for recently I have 2 proteins, with phenix.real_space_refine, the critical clashing score  20 level cannot be got (always higher than 20).

Best regards.


Smith

On Monday, October 5, 2015 2:52 PM, Smith Liu <[email protected]> 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" <[email protected]> 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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