[phenixbb] on ligand restraint

Smith Liu smith_liu123 at 163.com
Mon Oct 5 03:31:52 PDT 2015

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.


At 2015-10-05 14:12:39, "Pavel Afonine" <pafonine at lbl.gov> wrote:
Most likely wrong ligand CIF file.

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.


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
>> _______________________________________________
>> 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
>Unsubscribe: phenixbb-leave at phenix-online.org


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20151005/1bc51c68/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ATP.cif
Type: application/octet-stream
Size: 13022 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20151005/1bc51c68/attachment.obj>

More information about the phenixbb mailing list