​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: [email protected] <[email protected]> on behalf of [email protected] <[email protected]>
Sent: Tuesday, June 6, 2017 9:16 PM
To: Terwilliger, Thomas Charles
Cc: [email protected]
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@iphy.ac.cn

At 2017-06-07 10:32:14, "Terwilliger, Thomas Charles" <[email protected]> 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: [email protected] <[email protected]> on behalf of [email protected] <[email protected]>
Sent: Tuesday, June 6, 2017 8:19 PM
To: [email protected]
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@iphy.ac.cn