Re: [phenixbb] Something that came up on the CCP4 list...
Just for the record I've had it make a big difference a number of times as well with both refmac & shelx. I was under the impression that phenix.refine was "cleverly" allowing me to use that trick by just starring the add riding hydrogens in the def file however it seems not - something worth knowing! Simon On 16 Sep 2010, at 20:01, Phil Jeffrey wrote:
I've had it make a big difference in certain circumstances. And in other circumstances not so much. Definitely worth a try. I do not use the technique routinely.
Phil Jeffrey Princeton
On 9/16/10 11:49 AM, Simon Kolstoe wrote:
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Simon,
Just for the record I've had it make a big difference a number of times as well with both refmac & shelx. I was under the impression that phenix.refine was "cleverly" allowing me to use that trick by just starring the add riding hydrogens in the def file however it seems not - something worth knowing!
if you mean hydrogens { refine = individual *riding .... } then this is just tells "how to refine hydrogen atoms if present" and not to actually "add and refine". There is no way to build the template of parameters dynamically based on current inputs. So there will always be a bunch of parameters in your automatically generated parameter file that do not actually apply to your particular refinement run. For example, if you do not have H atoms in input PDB file then the whole block of parameters hydrogens { .... } will not make any different in your refinement run regardless whatever you specify there. Sorry for confusion. Pavel.
participants (2)
-
Pavel Afonine -
Simon Kolstoe