On Friday, 28 February 2020 11:19:37 PST Diana Tomchick wrote:
> If you deposit an mmCIF file that contains both the observed and calculated
> structure factors from your final round of refinement, then the PDB
> auto-validation reports the same (or so close to the same as to be
> negligible) R factors.
Yes, that's the "Depositor" line in the validation report.
The separate "DCC" line tries to recalculate from the model description.
It matches quite well if your model matches its default expectations,
but otherwise it can diverge. It's a useful check that you haven't made
some inadvertent mistake in preparing the deposition files, but beyond
that it is less useful than, say, confirming that the model refinement
can be reproduced by feeding it to PDB-Redo.
Ethan
> Phenix outputs all of this automatically for you if you click the correct
> radio button in the GUI.
> Diana
>
> **************************************************
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu>
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
>
> On Feb 28, 2020, at 12:51 PM, Ethan A Merritt
> <merr...@uw.edu<mailto:merr...@uw.edu>> wrote:
> EXTERNAL MAIL
>
> 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<mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of
> merr...@uw.edu<mailto: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
>
> ________________________________
>
> UT Southwestern
>
>
> Medical Center
>
>
>
> The future of medicine, today.
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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