Dear Tim and All,

For phenix.real_space_refine, there is no log file as output file. For the new official version of phenix10, I also have tried to add H for the phenix.real_space_refine. However rather than to decrease the clash, the clash score increased to about 40 from 30, with H addition by phenix.pdbtools before phenix.real_space_refine was run.

Thus I hope I can get more comments related to the issue.

Best regards.

Smith

On Monday, September 28, 2015 6:07 PM, Tim Gruene <[email protected]> wrote:

Dear Smith,

hydrogen positions are calculated from the geometry of the binding
environment. You can add them at any resolution.

Did you read the log file and judge the parameter settings in phenix? Did you
increase the number of refinement cycle to ease the transition to a new
version? Did you check the model in Coot to fix the problems?

Regards,
Tim

On Monday, September 28, 2015 01:21:21 AM Smith Lee wrote:
> Dear All,
> With the EM cryo data, I have compared the function of
> phenix.real_space_refine of Phenix10 and Phenix1.9-1692. For the
> Ramachandran favored, the new version is about 90%, the old version is
> about 92%. For the clashscore by Molprobity, the new version is about 30,
> the old version is about 20. Molprobity indicated the clashing atoms were
> systematically existing in the whole molecule, rather than on specific
> parts of the protein which may be indication of bad modelling. Clearly the
> clashscore of 30 is unacceptable. Will you please give some advise on how
> to improve the function of new version of Phenix, considering adding H was
> not suitable as for the resolution was poorer than 4.0 A? Smith

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Paul Scherrer Institut
Dr. Tim Gruene
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phone: +41 (0)56 310 5297

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