On Thursday, 27 February 2020 16:34:50 PST Alexander Aleshin wrote: > Ethan wrote: > - If you are not making claims about hydrogens but just want to > describe what you did during refinement, I'd go with taking them out > > I've noticed that REFMAC and Phenix use riding hydrogens to calculate the > refinement statistics, and their exclusion affects R/Rfree. As a result, it > is not clear what values should be reported.
> In my opinion, riding > hydrogens play same role as the TLS parameters, which we keep in a pdb > submission. So, I am not convinced their omission is a good idea. > I think PDB curators should provide a guidance how to deal with issues like > a resolution of anisotropic or incomplete data sets, riding hydrogens, > sequence numbering etc. Alex: You are right that the PDB auto-validation step of recalculating R factors from the deposited model and observed F's is far from perfect. I have not looked at the DCC source code, but my impression from the R factors it spits back at me during deposition: - it ignores TLS records - it ignores the header record specifying choice of solvent model - it does use scattering factors f' and f" from the mmcif coordinate file - I have no idea what it does with twinning descriptions As a result there is often a noticeable discrepancy between the R-factors from "Depositor" and "DCC" in the validation reports. > Regards, > Alex > > > > > On 2/27/20, 4:05 PM, "CCP4 bulletin board on behalf of Ethan A Merritt" > <CCP4BB@JISCMAIL.AC.UK on behalf of merr...@uw.edu> wrote: > [EXTERNAL EMAIL] > > On Thursday, 27 February 2020 15:35:05 PST Whitley, Matthew J wrote: > > > Hello all, > > > > > > > > I am nearly finished refining the structures of two mutant proteins > > from > > crystals that diffracted to very high resolution, 1 Å and 1.2 Å, > > respectively. Refinement was conducted in the presence of explicit > > hydrogens on the models. I am preparing to deposit these models into > > the > > PDB but am unsure about whether to retain or remove the hydrogens for > > deposition. On one hand, these hydrogens were explicitly used during > > refinement, so that makes me want to keep them, but on the other hand, > > they were added at theoretical positions by MolProbity’s reduce tool > > for refinement and were not positioned on the basis of experimentally > > observed electron density, so that makes me want to delete them from > > the > > experimental model. Which is the preferred option for this > > situation? > > > The order of operations you describe is unclear. > > If you explicitly refined hydrogens then their final positions are > indeed based on experimentally determined data. > The fact that you initially placed them into ideal geometry is not > really any different from the non-H atoms of individual protein residues > in your model, whose original positions were also based on known > stereochemistry. > On the other hand, if you mean that the hydrogens you used for > refinement were deleted and replaced during validation by Molprobity > (which I think it may do by default) that's not good. You should rather > keep the hydrogen positions from refinement, not the ones from Molprobity. > > Assuming (since this is ccp4bb) you refined with refmac... > - If you are at the level of investigating hydrogen positions, you may > want to consider taking the refinement into shelxl. > - If you are not making claims about hydrogens but just want to > describe what you did during refinement, I'd go with taking them out and > settling for the standard record in the resulting PDB file: > REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS > which looks like this in the corresponding mmcif file: > _refine.details 'Hydrogens have been added in their riding > positions' > Ethan > > > > > > > > Thanks, > > Matthew > > > > > > > > --- > > Matthew J. Whitley, Ph.D. > > Research Instructor > > Department of Pharmacology & Chemical Biology > > University of Pittsburgh School of Medicine > > > > > > > > > > ###################################################################### > > ## ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
