[phenixbb] phenix.map_to_model input mtz file failure --caution on using map_to_model with X-ray data
Tim Gruene
tim.gruene at psi.ch
Thu Jun 8 10:05:40 PDT 2017
Hi Ed,
including the 'free' reflections in the map for modelling does not taint the
value of Rfree. That is a misconception that i s very persistent (as prejudice
usually are). I believe it was Ian Tickle who formulated that when you simply
refine long enough towards convergence, all reflections excluded from refinement
will become independent, i.e. you can assign a new set for Rfree every time
you refine, if you wish so.
This concept is the reason why Rcomplete (the "better" equivalent to Rfree for
small data sets with < 10,000 unique reflections), introduced by Axel Brunger,
works, as we could demonstrate in doi: 10.1073/pnas.1502136112
So nothing to worry about when including all reflections in map calculations.
Cheers,
Tim
On Thursday, June 8, 2017 12:42:53 PM CEST Edward A. Berry wrote:
> Hi, Tom,
> Please forgive what may be a silly question from an outsider who hasn't
> really kept up with the crystallography literature or even all the Phenix
> newsletters- What is the evidence that including the free set in real space
> refinement biases R-free of the resulting model? Is this Rfree also biased
> when map coefficients use "fill-in" for the excluded free reflections (and
> is that what phenix.remove_free_from_map does?).
>
> My point is that literally excluding the free reflections, as opposed to
> substituting their values with Fc, will bias the free set toward grossly
> incorrect values (namely zero) and therefore greatly worsen R-free. Thus if
> the evidence for bias is that you get worse R-free when you exclude the
> free set, you have to think about how much of that difference results from
> bias towards the observed values (when the reflections are included) and
> how much is from bias towards zero (when the free set is excluded).
> (Again, I realize this may be all very well understood by the
> crystallography community and properly taken care of in phenix; I'm just
> asking for my own information) eab
>
> On 06/08/2017 07:28 AM, Terwilliger, Thomas Charles wrote:
> > Hi Wei,
> >
> >
> > I want to give a word of caution about how to use phenix.map_to_model on
> > crystallographic data...The bottom line is you should remove the test set
> > from your map coefficients before running phenix.map_to model on X-ray
> > data. Here is why:
> >
> >
> > phenix.map_to_model uses real-space refinement, which is refinement
> > against the map. If you supply map coefficients that include your test
> > reflections, then you will be refining against data that is in your test
> > set. This will make your Rfree invalid when you go back and refine your
> > model against the original crystallographic data.
> >
> >
> > To remove the test set from your map coefficients you can use:
> >
> >
> > phenix.remove_free_from_map map_coeffs=my_map_coeffs.mtz
> > free_in=my_data_file_with_freeR_flags.mtz
> > mtz_out=my_map_coeffs_no_free.mtz
> >
> >
> > Also note that phenix.map_to_model uses a fixed map (it does not do
> > density modification). Consequently for most crystallographic data at
> > moderate resolution or higher phenix.autobuild is going to do much better
> > than phenix.map_to_model.
> >
> >
> > All the best,
> >
> > Tom T
> >
> >
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> > ---------------------------- *From:* dingding830106 at 163.com
> > <dingding830106 at 163.com> on behalf of dancingdream at 163.com
> > <dancingdream at 163.com> *Sent:* Tuesday, June 6, 2017 9:16 PM
> > *To:* Terwilliger, Thomas Charles
> > *Cc:* phenixbb at phenix-online.org
> > *Subject:* Re:Re: [phenixbb] phenix.map_to_model input mtz file failure
> > Dear Thomas,
> > I use CAD to convert the labels from FDM->FWT, PHIDM->PHFWT, then submit
> > this job again (without map_coeffs_labels=... ), and everything seems ok.
> > Thank you very much for you help.
> > Best!
> >
> >
> > --
> > Wei Ding
> > P.O.Box 603
> > The Institute of Physics,Chinese Academy of Sciences
> > Beijing,China
> > 100190
> > Tel: +86-10-82649083
> >
> > E-mail: dingwei at iphy.ac.cn <mailto:wangli at moon.ibp.ac.cn>
> >
> > At 2017-06-07 10:32:14, "Terwilliger, Thomas Charles"
<terwilliger at lanl.gov> wrote:
> > Hi Wei,
> >
> >
> > I'm sorry for the trouble!
> >
> >
> > If you supply an MTZ file that has FWT,PHFWT or similar labels, then
> > you can skip the "labels=...." statement and it should run.
> >
> >
> > Let me know if that does not work!
> > All the best,
> >
> > Tom T
> >
> >
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> > ---------- *From:* phenixbb-bounces at phenix-online.org
> > <mailto:phenixbb-bounces at phenix-online.org>
> > <phenixbb-bounces at phenix-online.org
> > <mailto:phenixbb-bounces at phenix-online.org>> on behalf of
> > dancingdream at 163.com <mailto:dancingdream at 163.com>
> > <dancingdream at 163.com <mailto:dancingdream at 163.com>> *Sent:* Tuesday,
> > June 6, 2017 8:19 PM
> > *To:* phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> > *Subject:* [phenixbb] phenix.map_to_model input mtz file failure
> > Dear Phenix bb,
> > I intend to build a initial model by phenix.map_to_model. And the
> > command line is as follows: phenix.map_to_model_1.12rc0-2787
> > map_coeffs_file=../rep_dm.mtz map_coeffs_labels="'FP,SIGFP' 'PHIDM'
> > 'FOMDM'" seq_file=../resolve.seq is_crystal=True
> > use_sg_symmetry=True density_select=False truncate_at_d_min=True
> > and the feedback like this:
> > Sorry: No initial assignment made for map_coeffs. Labels used:
> > FP,SIGFP PHIDM FOMDM. Available labels: ['PHIB', 'FOM',
> > 'HLA,HLB,HLC,HLD', 'FP,SIGFP', 'PHIDM', 'FOMDM', 'FDM',
> > 'HLADM,HLBDM,HLCDM,HLDDM'] NOTE: grouped labels like 'FP,SIGFP' must
> > stay together,
> > have commas, and have no spaces. If they come from an MTZ file,
> > they must be in adjacent columns as well.
> > Suggested labels to use: PHIDM FOMDM
> > I try many other input format of map_coeffs_labels, such as
> > map_coeffs_labels="FP,SIGFP PHIDM FOMDM"
> > map_coeffs_labels=["FP,SIGFP PHIDM FOMDM"]
> > ... ...
> > but the result is the same. Dose anyone can tell me how to fix this
> > problem? Thank a lot.
> >
> >
> >
> >
> >
> > --
> > Wei Ding
> > P.O.Box 603
> > The Institute of Physics,Chinese Academy of Sciences
> > Beijing,China
> > 100190
> > Tel: +86-10-82649083
> > E-mail: dingwei at iphy.ac.cn <mailto:wangli at moon.ibp.ac.cn>
> >
> > _______________________________________________
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> > phenixbb at phenix-online.org
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>
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--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/104
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
GPG Key ID = A46BEE1A
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