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

Edward A. Berry BerryE at upstate.edu
Tue Jun 13 12:30:00 PDT 2017

```Thanks, Pavel,
I really appreciate your taking the time to generate the example.

While I agree with Tim and Ian that refinement to convergence should
remove the bias making it perhaps not a serious problem, my question was
in fact whether there is any bias immediately after the refinement.

I will need to study this example a bit, but one thing I notice is
that you are doing exactly what I was guessing, comparing Rfree
after real-space refinement with and without using the free set.
Then, I still think, we
>>> 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).

Things I need to look at-
What are R and R-free for the original refined model
What are R and R-free after shaking (did RSR lower R but not Rfree, or did it raise Rfree?
What if RSR is done using a map made with fill-in strategy?

Ed

On 06/13/2017 02:15 PM, 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 ofdancingdream 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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