[phenixbb] phenix.ready_set hydrogens not compatable with coot library

Jeff Headd jjheadd at lbl.gov
Mon Aug 23 13:30:42 PDT 2010

Hi Phil,

By default in PHENIX hydrogens are treated as riding model, and as you
say they are important for preventing steric clashes from developing
during refinement.  When used in refinement, however, it is very
important to include them in your deposition because how their
B-factor terms are specified and handled is essential to understanding
where the final model came from.  Further, the final position of some
of the hydrogens is difficult to predict (such as a rotatable methyl
group), so knowing what the final positions are for such hydrogen
atoms is necessary to account for the deposited model and refinement
statistics.  Without deposition atomic positions and B-factor
information for H atoms will be lost.  I don't think that having them
in your model implies that you can see them necessarily, but rather
implies that you know with fairly high accuracy where they are
(assuming your heavy atom positions are correct) and thus used them to
arrive at your final model.

When using Coot from the PHENIX GUI, there is an option to turn the H
atoms off in the display if you do find them to clutter the screen too
much.  Showing them in Coot can be useful, though, as Coot is able to
display Probe dots to help in guiding hand-correction of problem areas
in your model.


On Mon, Aug 23, 2010 at 1:08 PM, Phil Evans <pre at mrc-lmb.cam.ac.uk> wrote:
> Coming from using Refmac I'm slightly puzzled by the philosophy here. By  default (I believe) Refmac always adds riding hydrogens for the refinement but doesn't output them in the refined PDB files. This seems to me to be the right thing to do. I don't see any reason for not including Hs in refinement since you know where most of them are relative to the heavy atoms, and they will (maybe marginally) improve things. On the other hand I don't normally want them cluttering up the display in Coot (maybe because I'm just not used to them), and I certainly don't want to include them in my PDB deposition, since I don't think they are an independent part of the model, and including them would imply I can see them. They are I suppose useful in bump checks, but I would just add them back for that purpose
> Phil
> On 23 Aug 2010, at 20:09, Joseph Noel wrote:
>> Hi All,
>> Indeed even the latest COOT still relies on the old PDB format and hydrogens fly. Its probably not prudent to use hydrogens in refinement then remove them and add back each time. Kind of defeats the purpose of using them in the first place. Until COOT is updated I found a pretty easy way around things as long as you have access to the internet. Just use the MOLPROBITY site (http://molprobity.biochem.duke.edu/). In addition to it being a fantastic tool for really cleaning up structures, you can quickly upload your refined file from Phenix with hydrogens, then hit the button to downgrade to PDB v23. It creates the appropriate file with renamed hydrogens that work great in COOT. You can then re-upload the COOT rebuilt model and it will "upgrade" naming to the latest PDB version. Download that file and there you go for Phenix refinement. Sounds like a bit but very fast and easy to implement until COOT is upgraded.
>> Joe
>> ___________________________________________________________
>> Joseph P. Noel, Ph.D.
>> Investigator, Howard Hughes Medical Institute
>> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
>> The Salk Institute for Biological Studies
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