[phenixbb] phenix.map_to_model input mtz file failure --caution on using map_to_model with X-ray data

Dale Tronrud detBB at daletronrud.com
Tue Jun 13 11:30:30 PDT 2017


   The difference of opinion between Tim and Pavel is that Tim is
assuming that the real space refinement will be followed by reciprocal
space refinement with the test set withheld.  This will be the case for
model building in Coot which is usually followed by full-blown
refinement in one of the classic packages.  The story is different for
cryo-EM maps where there is no reciprocal space refinement.

   While I would question the wisdom of using R values at all, when both
the model and the original data live in real space, people do seem to
like it.  I think it would be better to develop cross-validation metrics
designed with cryo-EM's experimental setup in mind and not simply reuse
those designed for diffraction experiments.

Dale Tronrud

On 6/13/2017 11:15 AM, Pavel Afonine wrote:
> Hi Ed,
> 
> Including free-r reflections into map calculation and then using such
> map in real-space refinement of entire model will affect Rfree. Here is
> a simple example that illustrates my statement, step-by-step:
> 
> 1) Get data and model from PDB:
> 
> phenix.fetch_pdb 1f8t --mtz
> 
> 2) Compute two 2mFo-DFc maps: one includes all reflections the other one
> has no free-r terms:
> 
> phenix.python run.py 1f8t.{pdb,mtz}
> 
> This will create an MTZ file (map_coeffs.mtz) that contains Fourier map
> coefficients for both maps.
> 
> 3) Shake model a bit:
> 
> phenix.dynamics 1f8t.pdb number_of_steps=500
> 
> 4) Run real-space refinement using two maps:
> 
> phenix.real_space_refine map_coeffs.mtz 1f8t_shaken.pdb
> label="work,PHIwork" ncs_constraints=false output.file_name_prefix=work
> 
> phenix.real_space_refine map_coeffs.mtz 1f8t_shaken.pdb
> label="all,PHIall" ncs_constraints=false output.file_name_prefix=all
> 
> 5) Compute R-factors using data and real-space refined models:
> 
> phenix.model_vs_data 1f8t.mtz all_real_space_refined.pdb
>     r_work(re-computed)                : 0.2419
>     r_free(re-computed)                : 0.2441
> 
> phenix.model_vs_data 1f8t.mtz work_real_space_refined.pdb
>     r_work(re-computed)                : 0.2444
>     r_free(re-computed)                : 0.2756
> 
> The result is self-explicable and is inline with Tom's reply to Wei.
> 
> All files necessary to reproduce calculations above are here:
> http://cci.lbl.gov/~afonine/tmp/
> 
> All the best,
> Pavel
> 
> 
> On 6/8/17 10:05, Tim Gruene wrote:
>> 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
>>>>
>>>>
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> --------------------------------------------------------------------------
>>>> ---------------------------- *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
>>>>     
>>>>     
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ----------------------------------------------------------------------
>>>>     ---------- *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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