# [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 12:47:46 PDT 2017

```Another test- do RSR, excluding the free set, on the fully refined
model without shaking. You cannot expect to decrease R or R-free,
but if R-free is not being biased, at least it should not go up.
If the free reflections are being biased toward zero's, Rfree
should increase with this.
Ed

On 06/13/2017 03:30 PM, Edward A. Berry wrote:
> 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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>>>>> phenixbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
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