The R-factor difference of 0.0004 is what you have to expect as the result of writing the coordinates, B-factors, and occupancies to the PDB file. In memory floating-point numbers have >= 12 digits precision (we use double precision for almost everything); in the PDB file you have only 7 digits for the coordinates and just 5 digits for the B-factors and occupancies.<div>
Ralf<br><br><div class="gmail_quote">On Fri, Mar 23, 2012 at 9:49 AM, Christian Roth <span dir="ltr"><<a href="mailto:christian.roth@bbz.uni-leipzig.de">christian.roth@bbz.uni-leipzig.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Nat,<br>
<br>
I agree with you that the difference is very small and likely negligible. I<br>
just asked for curiosity if there might be any reason for this behaviour.<br>
<br>
Christian<br>
<br>
Am Donnerstag 22 März 2012 23:07:33 schrieb Nathaniel Echols:<br>
> On Thu, Mar 22, 2012 at 2:54 PM, Christian Roth<br>
><br>
> <<a href="mailto:christian.roth@bbz.uni-leipzig.de">christian.roth@bbz.uni-leipzig.de</a>> wrote:<br>
> > I am not sure I looked into the polygon. In the log it is stated that the<br>
> > R values are calculated after a resolution and sigma cutoff applied. If<br>
> > I understood the log correctly the values taken from the pdb header are<br>
> > without sigma cutoff. Maybe thats the reason for the difference. Does<br>
> > modelvsdata somewhere print the values without cutoff in the log file? I<br>
> > did not find it. However does this mean till firsst OHS in phenix refine<br>
> > a default cutoff is used and in than throughout the refinement no coutoff<br>
> > is used anymore?<br>
><br>
> After spending some time looking at similar cases today I am not sure<br>
> myself what is going on. I do not think a sigma cutoff is applied,<br>
> unless perhaps the PDB header indicates that one was used previously<br>
> (this is a thoroughly antiquated practice). However, outlier<br>
> filtering appears to be used throughout. I found one example where<br>
> nearly 4000 reflections have amplitudes of zero (which is surely not<br>
> correct), and are discarded as outliers in phenix.refine. This<br>
> reduces R-free by 0.03. In model_vs_data, the same numbers appear<br>
> twice:<br>
><br>
> Model_vs_Data:<br>
> r_work(re-computed) : 0.2030<br>
> r_free(re-computed) : 0.2639<br>
> ...<br>
> After applying resolution and sigma cutoffs:<br>
> n_refl_cutoff : 31257<br>
> r_work_cutoff : 0.2030<br>
> r_free_cutoff : 0.2639<br>
><br>
> But this totally contradicts what I told you earlier, sorry. I was<br>
> assuming that they would be different.<br>
><br>
> I do have a general piece of advice, however: ignore the discrepancy,<br>
> and just report the value that came out of refinement (because that is<br>
> what will end up in the PDB). The difference in your case is<br>
> relatively small, probably less than what you'd see if you calculated<br>
> R-factors with (for instance Refmac), because of different<br>
> implementations of bulk solvent correction and scaling, etc.*. (Even<br>
> different versions of Phenix aren't guaranteed to yield identical<br>
> R-factors, due to low-level changes.) Considering how difficult it<br>
> can be to reproduce the statistics in published structures, a change<br>
> of 0.0004 isn't enough to worry about.<br>
><br>
> -Nat<br>
><br>
> * <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906258/?tool=pubmed" target="_blank">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906258/?tool=pubmed</a><br>
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><br>
<br>
<br>
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</blockquote></div><br></div>