Re: [phenixbb] on ligand restraint

Smith

From the comments in the file, you generated the ATP restraints with 1.9-1692. I redid the command with 1.10-2155 and the restraints were better. Clearly, the program has improved in the 13 months that 1.9 was released and you should stop using it in preference for 1.10.

Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Oct 5, 2015 at 3:31 AM, Smith Liu wrote:

Dear Pavel,

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.

Smith

At 2015-10-05 14:12:39, "Pavel Afonine" wrote:

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" 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?

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