In the fascinating current discussion on the ccp4 list Pavel said:
Dear Ed,
no, if you start with model that has no hydrogens, they will not be generated internally.
Pavel.
On 9/15/10 2:58 PM, Ed Pozharski wrote:
Sure. But if I start with model that has no hydrogens, they will be generated but not passed to the output, right. just like refmac.
On Wed, 2010-09-15 at 14:52 -0700, Pavel Afonine wrote:
Dear Ed,
On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote:
So the riding hydrogen model is imperfect. At least with phenix.refine you can measure it, unlike the default behavior of REFMAC. (But you can tell it to write hydrogens out, I believe).
My impression is that default behavior of phenix.refine is the same - I had to change parameters to include hydrogens in the output. No, if your input file contains H atoms, the output file will contain
On 9/15/10 2:47 PM, Ed Pozharski wrote: them too (in phenix.refine). You don't have to change any parameters for this.
Pavel.
Could I just seek some clarification? I was under the impression that phenix.refine calculated riding hydrogens by default and took these into account as a restraint on the geometry? Simon
Hi Simon,
Could I just seek some clarification? I was under the impression that phenix.refine calculated riding hydrogens by default and took these into account as a restraint on the geometry?
if you want hydrogen atoms to be used in refinement (as "riding model" or explicit) your need to make sure the PDB file that you give to phenix.refine contains H atoms. That is you need to add them using programs like phenix.reduce or phenix.ready_set or using corresponding functionality in the GUI. phenix.refine will not add them internally as part of refinement IF hydrogen atoms are NOT present in input PDB file. Adding hydrogen atoms as 'riding model' does not add any refinable parameters, but the scattering contribution from them is included most of the time. This is why we do not use H atoms silently but require them to be in input PDB file - simply to make sure the reported statistics (such as R-factors) is easily reproducible. All the best! Pavel.
So just to clarify further - if i am having problems with the final geometry of a model (eg clashscore as reported by molprobity), is it an appropriate trick to add hydrogens and then refine in phenix.refine using the riding hydrogens option, or does this not really change anything? Simon On 16 Sep 2010, at 14:26, Pavel Afonine wrote:
Hi Simon,
Could I just seek some clarification? I was under the impression that phenix.refine calculated riding hydrogens by default and took these into account as a restraint on the geometry?
if you want hydrogen atoms to be used in refinement (as "riding model" or explicit) your need to make sure the PDB file that you give to phenix.refine contains H atoms. That is you need to add them using programs like phenix.reduce or phenix.ready_set or using corresponding functionality in the GUI.
phenix.refine will not add them internally as part of refinement IF hydrogen atoms are NOT present in input PDB file.
Adding hydrogen atoms as 'riding model' does not add any refinable parameters, but the scattering contribution from them is included most of the time. This is why we do not use H atoms silently but require them to be in input PDB file - simply to make sure the reported statistics (such as R-factors) is easily reproducible.
All the best! Pavel. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Simon,
So just to clarify further - if i am having problems with the final geometry of a model (eg clashscore as reported by molprobity), is it an appropriate trick to add hydrogens and then refine in phenix.refine using the riding hydrogens option, or does this not really change anything?
depending on what kind of geometry problems you have, adding and refining with "riding" hydrogens should help to improve the geometry. If (for whatever reason) it doesn't help, please contact me off-list and I will investigate. Pavel.
participants (2)
-
Pavel Afonine -
Simon Kolstoe