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

-- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - OFLC/107 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A

Typically, if clashes don't get resolved automatically it means bits of model where clashes occur are trapped in local minima that cannot be escaped by gradient-driven minimization. Try SA refinement or fix manually, then re-run your usual refinement. Pavel On 9/27/15 18:21, 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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