- phenixbb - phenix-online.org

phaser MR
by sbiswas2＠ncsu.edu 27 Jul '09

27 Jul '09

Hi all, I was trying to solve a structure by molecular replacement. I scaled the data in P4222 space group (resolution 2.7A) with two molecules in the assymmetric unit (molecule A and B) I ran phaser with my model and got a Zscore of 5.1. When I look at the map that I got from phaser I could easily see good electron density for both molecules, However upon inspection of the electron density map there were considerable interaction or clashes with molecule B and a symmetry atom. Molecule A had no clashes however with the symmetry atoms. I was wondering if anyone knows how to resolve this. Could it be a problem of space group. The statistics are good for space group P4222 and the I/sigI was good till 2.7A. Any advice is appreciated, Shya

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question about SAD+MR
by crystallogrphy 24 Jul '09

24 Jul '09

Dear all, I have a Se-Met SAD data which diffracted to 2.8A (peak wavelength). The space group is P1. The map from SAD autosol and autobuild still gives crappy map, I can only see one continous alpha-helix density with all other density fragmented and difficult to identify. I suppose it is because of high mosaicity (1.5), low data redundency, and some radiation damage. Now I want to use mocular replace (sequence identify ~0.26) plus SAD data to give better map. 1. The result from MR is shown below and the density is poor as the sole SAD map: REMARK Log-Likelihood Gain: 121.374 REMARK RFZ=3.4 TFZ=100.0 PAK=0 LLG=29 RFZ=3.7 TFZ=5.4 PAK=0 LLG=69 RFZ=6.1 TFZ=4.0 PAK=0 LLG=97 RFZ=5.6 TFZ=5.0 PAK=0 LLG=118 LLG=121 2. I then tried to combine MR model and SAD data set phenix.autosol seq_file=zntb-sd.seq sites=14 atom_type=Se data=output-peak.sca sg="P1" cell="44.355 56.687 58.451 61.061 82.013 82.740" resolution=3.0 input_partpdb_file=AutoMR_run_1_/MR.1.pdb The program failed to run with such error message: Failed to carry out AutoSol_score_ha_solutions: [Errno 2] No such file or directory: 'AutoSol_run_3_/TEMP0/phaser_mtz.hand.mtz' I do not know where to get this phaser.mtz.hand.mtz file or how to generate it. Does anyone know? -- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: qunwan1(a)gmail.com lab phone: 216-368-3337

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new gui on osx (10.5)
by Miguel Ortiz Lombardia 24 Jul '09

24 Jul '09

Dear all, We would like to run the new phenix GUIs from a remote computer. Both server and clients are OSX 10.5 (leopard) and they have the same versions of software (X11, python, phenix... all them pretty new versions) When trying to do so, we invariably get this error: This program needs access to the screen. Please run with 'pythonw', not 'python', and only when you are logged in on the main display of your Mac. I have searched the internet for similar problems and I found an old (one year) unresolved question on the same/similar issue: http://www.phenix-online.org/pipermail/phenixbb/2008-July/001129.html In our case, the /usr/local directory is not mounted over the NFS, it is local. As in that case, though, changing the LIBTBX_PYEXE_BASENAME to pythonw (for example in the phenix.autosol_gui wrapper) did not solve the issue. However, it is not clear to me that this variable has to be changed in a single place: it is found in many files. My question is: was this issue solved and I missed that? If not, anyone has a clue on how to solve the problem? Just to make it clear, the GUIs work perfectly locally in the server computer, that is, if not exported. Thanks a lot! Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

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sigma cutoff
by dziuba＠amu.edu.pl 24 Jul '09

24 Jul '09

Hi, According to the Phenix manual, phenix.refine uses no sigma cutoff by default. Since I haven't changed this manually, why do I see in my pdb file MIN(FOBS/SIGMA_FOBS) 1.340? Thanks for help, Karolina

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ENSEmble parameters when the model is an EM map
by Peter Grey 24 Jul '09

24 Jul '09

Dear benevolent experts, I am trying to use Phaser for molecular replacement with EM-map as a model. The EM map, originally in a small P1 cell, was put in large P1 using CCP4's MAPROT and a mask that was defined by a certain cut-off level. Could you please advise me how to derive the EXTEnt and CENTre parameters needed for ENSEmble building ? Does the simple way of giving the size of the original P1 as the EXTEnt and its centre as CENTre sound reasonable ? I would be grateful for any advice and comments, Peter.

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anisotropic ADP factor refinement and optimize_wxc
by Joyce, Gordon M. (NIH/NIAID) [F] 22 Jul '09

22 Jul '09

Dear All, I have just recently started using phenix.refine and I hope I can get some advice. I am trying to refine my structure with anisotropic ADP factors while also optimizing the weighting parameters.When I give the following command, anisotropic refinement is carried out but optimization is not carried out as far as I can see (ie the rms bond and angles are not reduced, which is one of my concerns at the moment). phenix.refine protein1.pdb 072109checks.mtz ordered_solvent=true strategy=individual_adp adp.individual.anisotropic="not element H" optimize_wxc=true --overwrite pdb output values REMARK Start: r_work = 0.1952 r_free = 0.2388 bonds = 0.015 angles = 1.646 REMARK Final: r_work = 0.1413 r_free = 0.2448 bonds = 0.015 angles = 1.646 If I give the following command, optimization occurs and rms bond and angle values decrease. phenix.refine protein1.pdb 072109checks.mtz optimize_wxc=true --overwrite REMARK Start: r_work = 0.2048 r_free = 0.2388 bonds = 0.015 angles = 1.646 REMARK Final: r_work = 0.1917 r_free = 0.2352 bonds = 0.009 angles = 1.301 Is it possible to refine both anisotropic B factors and optimize ADP factors in the same run. Any advice would be great. Thanks, Gordon

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Phenix.refine coordinate error estimate discrepancies
by Phil Jeffrey 21 Jul '09

21 Jul '09

There seems to be a large discrepancy between the likelihood-based coordinate error estimate depending on whether the intensities or structure factor magnitudes are used, which doesn't make any sense to me. If I do: % phenix.refine rebuild.pdb data_withI.mtz phenix.refine picks up Imean and SigImean from the MTZ and refines the structure xray_data { file_name = "data_withI.mtz" labels = "IMEAN,SIGIMEAN" r_free_flags { file_name = "data_withI.mtz" label = "FreeR_flag" test_flag_value = 0 } then I get: | maximum likelihood estimate for coordinate error: 1.39 A But if I create an MTZ file without the intensities by using CAD on the original file, and use the same coordinate file: % phenix.refine rebuild.pdb data_withoutI.mtz phenix.refine picks up the structure factors instead: xray_data { file_name = "data_withoutI.mtz" labels = "F,SIGF" r_free_flags { file_name = "data_withoutI.mtz" label = "FreeR_flag" test_flag_value = 0 } } then this seems to be the right ballpark for a 1.75 Angstrom structure.... | maximum likelihood estimate for coordinate error: 0.28 A Similar R-factors, but there is a factor of 10 difference in the scale reported here: I's: r_work= 0.2266 r_free= 0.2570 ksol= 0.41 Bsol= 50.00 scale= 0.097 F's: r_work= 0.2221 r_free= 0.2557 ksol= 0.41 Bsol= 50.00 scale= 0.965 Version: 1.4 Release tag: 3 cctbx tag: 2008_12_07_1353 Platform: mac-intel-osx osx-10.5.6 User: phil Cheers, Phil Jeffrey Princeton

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Assertion Error when using kicked maps in solvent update
by Schubert, Carsten [PRDUS] 21 Jul '09

21 Jul '09

Hi In 1.4.106 I get the following Assertion Error when I use kicked maps (refinement.ordered_solvent.use_kick_maps=True) in the solvent update section: Traceback (most recent call last): File "/raidnet/xdata1/programs/phenix-1.4-106/phenix/phenix/command_line/refi ne.py", line 19, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/raidnet/xdata1/programs/phenix-1.4-106/phenix/phenix/refinement/comman d_line.py", line 89, in run call_back_handler=call_back_handler) File "/raidnet/xdata1/programs/phenix-1.4-106/phenix/phenix/refinement/driver .py", line 1125, in run call_back_handler = call_back_handler) File "/raidnet/xdata1/programs/phenix-1.4-106/phenix/phenix/refinement/strate gies.py", line 358, in refinement_machine log = log) File "/raidnet/xdata1/programs/phenix-1.4-106/cctbx_project/mmtbx/solvent/ord ered_solvent.py", line 205, in __init__ use_kick_map = self.params.use_kick_maps).peaks_mapped() File "/raidnet/xdata1/programs/phenix-1.4-106/cctbx_project/mmtbx/solvent/ord ered_solvent.py", line 394, in find_peaks log = self.log) File "/raidnet/xdata1/programs/phenix-1.4-106/cctbx_project/mmtbx/find_peaks. py", line 98, in __init__ crystal_gridding_tags = fft_map.tags() File "/raidnet/xdata1/programs/phenix-1.4-106/cctbx_project/cctbx/maptbx/__in it__.py", line 152, in tags return crystal_gridding_tags(self) File "/raidnet/xdata1/programs/phenix-1.4-106/cctbx_project/cctbx/maptbx/__in it__.py", line 158, in __init__ assert gridding.symmetry_flags() is not None AssertionError Running from the same .def file w/o kicked maps works fine. Let me know if you need more info to debug this. Cheers, Carsten

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Duration of a phenix.elbow run
by Dirk 21 Jul '09

21 Jul '09

Hi, I'm trying to create restraints for a carbohydrate ligand using phenix.elbow. If I run it without the --opt command everything works fine, but I'm not completely happy with the geometry of my ligand after refinement. I tried to get an optimized cif by using --opt command, but the program just runs up to the following output: MoleculeClass : H:38 C:23 N: 1 O:19 (PDB format) 81 atoms 83 bonds 151 angles 238 dihedrals -------------------- Time Energy delta E RMS Max Step size and then nothing happens for several hours. Does the optimization needs such a long time and if I let it run overnight (or perhaps longer) I will get an output or is something going wrong? The input is a pdb (I tested several) and I tried both the stable phenix release (1.3) and the current version (1.4). Any help would be very appreciated Thanks Dirk

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Unable to produce kicked maps
by Schubert, Carsten [PRDUS] 17 Jul '09

17 Jul '09

Hi , I am trying to make some kicked maps in 1.4.106. At the end of the run all I am getting is Sorry: Duplicate mtz_label_amplitude FOFCWT Any workaround, except not to use kicked maps? Here the diff_params output for easer debugging. Cheers Carsten <<diff.def>>

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autosol
by sbiswas2＠ncsu.edu 16 Jul '09

16 Jul '09

Hi, I was trying to run autosol using gui however it crashed with the following message: Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT Is this again a version problem? I am running version 1.4-6 Any help will be appreciated, Shya

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rigid body refinement in phenix.refine
by Pavel Afonine 16 Jul '09

16 Jul '09

To PHENIX users who asked about this: I recall several people (unfortunately, I don't remember who exactly) asked me about the details of rigid-body refinement implementation in phenix.refine (MZ protocol) and I promised to let them know when the corresponding paper is published. So here it is: J. Appl. Cryst. (2009). 42, 607-615 Automatic multiple-zone rigid-body refinement with a large convergence radius P. V. Afonine, R. W. Grosse-Kunstleve, A. Urzhumtsev and P. D. Adams http://journals.iucr.org/j/issues/2009/04/00/dd5048/index.html Pavel.

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error message
by zachcp 15 Jul '09

15 Jul '09

A Python error was detected. This is almost certainly a bug; please send an email containing this message to phenixbb(a)phenix-online.org so we can fix it. Thanks! SorryException : No array of observed xray data found. Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Xtriage.py", line 158, in OnExcept raise event.data SorryException: No array of observed xray data found.

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Average B-factor and ML error
by Leo Sazanov 15 Jul '09

15 Jul '09

Hi, phenix.refine outputs "WILSON B" value into PDB header after refinement, which is not the same as average B-factor of all the atoms in the structure, and not exactly the same as Wilson B-factor from SCALA scaling. How exactly is Wilson B-factor for phenix header calculated and would it be possible to output there also the average B-factor of all the atoms in the structure? Also, deposition into PDB requires only Luzzati coordinate errors, while phenix produces only ML based ones. Presumably ML estimate is better than Luzzati?, but it looks like often people just ignore PDB input for errors. It seems that it would it be useful in future to have ML option in the PDB submission process? Or should Phenix produce Luzzati errors as well? (I know that one can calculate av. B-fac in other programs or ask PDB to add some data to the deposition, but if the idea is to streamline the process...) Thanks, -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915 -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Anyone have a phenix.resolve script for after Phaser ?
by Phil Jeffrey 15 Jul '09

15 Jul '09

Although my usual m.o. is SHELX -> SHARP I'm exploring HYSS -> PHASER -> RESOLVE to see if the maps are any more interpretable. I think I've got good scripts for the first two steps but I'm not sure about my resolve script which stands at: phenix.resolve << EOD hklin myp3_auto.mtz LABIN FP=F SIGFP=SIGF PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD hklout resolve.mtz solvent_content 0.45 seq_file myp3.pir EOD This runs, but I could not tell from delving into the documentation if this was ideal or not. Thanks Phil Jeffrey (a Luddite and not using the GUI) Princeton

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Re: [phenixbb] refine occupancy of partially overlapping ligands
by Chris Ulens 14 Jul '09

14 Jul '09

Hi, I'm trying to refine the occupancy of 2 ligands that occupy the same binding pocket in 2 *partially* overlapping orientations. Let's assume I would define the ligands in 2 separate "chains" termed A and B. Could the experts point me to the proper syntax to define the correct group restraints to refine the occupancy? Thank you. Chris +++++++++++++++++++++++++++++++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium Tel +32 16 345812 Fax +32 16 345699 Telepathy 2.69 GHz +++++++++++++++++++++++++++++++

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can't find phaser_mtz.hand.mtz?
by Pei-Chun Lin 14 Jul '09

14 Jul '09

Hi, I am the beginner of crystallography and have a 3.5A map generated by MAD method using phenix GUI. I already traced and built 2/3 of my protein. I wish to use this partial model combined with SAD to generate a new map and see if the new map can help me to deal with the rest of the structure. Does it sound reasonable to you? However, after running AutoSol. I got this error message: Failed to carry out AutoSol_score_ha_solutions: [Errno 2] No such file or directory: 'AutoSol_run_1_/TEMP0/phaser_mtz.hand.mtz' What should I do now? Can't phenix automatically calculate it? PC _________________________________________________________________ Windows Live™: Keep your life in sync. Check it out! http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t1_allup_explore_012009

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tightening geometry
by Patrick Loll 10 Jul '09

10 Jul '09

Hi, I'm a little baffled. We have a 3 Å structure, and while the R values seem OK, I'd like to tighten up the rmsd values for the geometry. However, altering wxc_scale seems to have no effect. Specifics: In a clean directory, I run the following command phenix.refine X.mtz Y.pdb Z1.cif Z2.cif Z3.cif wxc_scale=0.??? strategy=group_adp (the cif files are libraries for different ligands) When I vary wxc_scale from 0.5 to 0.005, the geometry doesn't change at all, which makes no sense to me: For wxc_scale=0.5 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 For wxc_scale=0.05 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 For wxc_scale=0.005 r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151 ...you get the idea. These were run with phenix-1.4-3. With phenix-1.4-56, we get subtly different r values, but the bonds and angles numbers are the same as shown above (to 3 decimal places!), and the numbers don't change upon changing wxc_scale. Am I missing something here? Is there a better way to tighten up the geometry? Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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Re: [phenixbb] source of fobs for refinement after AutoSol
by Tom Terwilliger 09 Jul '09

09 Jul '09

Hi James, Yes, that is correct. However if you want...you can just go on to AutoBuild and build a new model from scratch and generate a set of free R flags there, supplying your data as data=mydata.sca. I would recommend this anyway because AutoBuild makes a much better model than AutoSol, and including the model from AutoSol doesn't necessarily help (and can make it worse if the AutoSol model is really incomplete, such as from secondary- structure-only model-building). I use the AutoSol model-building just to see if things are going well and then I throw that model away. This is also the default when you use "after_autosol=True" in AutoBuild and when you run the AutoBuild GUI after running AutoSol. It is convenient to use the data and freeR in in exptl_fobs_phases_freeR_flags_*.mtz from AutoSol but you don't have to. The key of course is: once you refine a model and want to use that model further...you must use the set of free R flags used in that original refinement from then on. If you throw away that model and start from scratch you can also make a new set of free R flags. The hexdigest REMARK in your PDB file from phenix.refine helps you make sure that this is done correctly. All the best, Tom T On Jul 9, 2009, at 8:35 AM, James Whittle wrote: > Dear Tom: > > Ok. Thanks for the quick response! > > I should run then run AutoSol again to get this file, and it will > have the HL coefficients in it? > > --James > > > On Jul 9, 2009, at 10:13 AM, Tom Terwilliger wrote: > >> Hi James, >> >> As you are expecting, in AutoSol the file >> exptl_fobs_phases_freeR_flags_*.mtz normally contains the >> experimental Fobs and free R flags for refinement, along with >> phases and HL coefficients from the experimental phasing. >> >> However if an anisotropy correction is applied to the data, then by >> default no refinement is done in AutoSol and no >> exptl_fobs_phases_freeR_flags_*.mtz file is created. This is to >> ensure that refinement is not carried out against anisotropy- >> corrected data (you want to refine against the original data, and >> have phenix.refine apply an anisotropy correction as part of >> refinement). >> >> If you supply >> >> input_refinement_file=my_data.sca >> >> then my_data.sca will be used for refinement and an >> exptl_fobs_phases_freeR_flags_*.mtz will be created. Note that >> my_data.sca can be identical to your input data file if you want. >> I am guessing that in your case an anisotropy correction was >> applied to the data in this way. >> >> I hope that helps! >> -Tom T >> ps. I am thinking of changing the default to make >> input_refinement_file automatically defined if an anisotropy >> correction is applied so that you don't have to do this... >> >> On Jul 9, 2009, at 7:55 AM, whittle wrote: >> >>> Dear all, >>> >>> I have a question regarding the output of AutoSol. >>> >>> I've run AutoSol, using the data directly from scalepack as a .sca >>> file, >>> and would like to now begin refining the structure I've built. >>> >>> There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the >>> AutoSol directory. Isn't this the right file to use? Since it's not >>> there, is it proper to use the phaser_2.mtz file for phenix.refine? >>> >>> --James >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov >> PHENIX web site: http:www.phenix-online.org >> ISFI Integrated Center for Structure and Function Innovation web >> site: http://techcenter.mbi.ucla.edu >> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB >> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb > Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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source of fobs for refinement after AutoSol
by whittle 09 Jul '09

09 Jul '09

Dear all, I have a question regarding the output of AutoSol. I've run AutoSol, using the data directly from scalepack as a .sca file, and would like to now begin refining the structure I've built. There seems to be no exptl_fobs_phases_freeR_flags_*.mtz file in the AutoSol directory. Isn't this the right file to use? Since it's not there, is it proper to use the phaser_2.mtz file for phenix.refine? --James

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2010 Gordon Conference on Diffraction Methods
by Andrew Leslie 02 Jul '09

02 Jul '09

The Gordon Research Conference on Diffraction Methods in Structural Biology will be held at Bates College in Lewiston, Maine, from July 18-23, 2010. As in the past, the program will include the latest developments in methodology covering all aspects of macromolecular crystallography, from crystallisation to model refinement and validation. We are currently preparing a preliminary program for the meeting, and would welcome suggestions for particular topics (with or without speakers). Please Email your suggestions to Andrew Leslie (andrew(a)mrc-lmb.cam.ac.uk) or Ana Gonzalez (ana(a)slac.stanford.edu). Andrew and Ana

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map output by phenix.refine
by 丁玮 02 Jul '09

02 Jul '09

Hi Pavel, Thank you for responding to my question so eloquently. But there are still something confusing me. First of all, when I used coot to open the "_map_coeffs.mtz", only two maps were displayed in the window,not four? Second, how to choose the maps coefficients? In phenix documentation, we konw that any specified coefficients can be set, for example: 2mFo-DFc, 2.7mFo-1.3DFc, Fo-Fc, 3Fo-2Fc. but it do not tell us why we should choose different coefficients. Thanks a lot. dream830106

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GUI problems
by Phil Evans 01 Jul '09

01 Jul '09

Hi I've just installed the Linux 64-bit version 1.4-105 on a CentOS5 machine, and I get a lot of errors in starting up the GUI. What am I missing? Also is it possible to install both the 32-bit & 64-bit versions together: I know it works for the executables in build/intel- linux-2.6 build/intel-linux-2.6-x86_64, but does that mess up the gui? It's OK on the command line Phil

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map output by phenix.refine
by Pavel Afonine 30 Jun '09

30 Jun '09

Hi Everyone, I think it's time to review this subject since it is one of the most frequently asked questions. Ironically, I think this is because we tried to make it as clear as possible -:) So, what kind of maps phenix.refine outputs by default? phenix.refine outputs two types of maximum-likelihood weighted maps (or, in other words, sigmaa-weighted maps): 2mFo-DFc and mFo-DFc. Now, as many of you noticed, the MTZ file with map coefficients "_map_coeffs.mtz" contains in fact four maps: 2mFo-DFc and mFo-DFc, and "filled" 2mFo-DFc and mFo-DFc (in fact fo-fc maps should be nearly identical; actually I have to fix it and not write identical fo-fc maps). The first two maps are computed using original Fobs (Fo), and the last two maps are computed using "filled Fobs", that is the original Fobs where missing reflections are "filled" with DFc. It is well known (I can spell a long list or references) that the data incompleteness affects the map quality, and sometimes, certain types of data incompleteness can *severely* distort maps. A possible solution (in order to reduce this negative effect) is to "model" missing Fobs somehow. One possibility is just to put in DFc in place where Fobs is missing, or as suggested by the classics, one can use <Fobs> taken in a resolution bin around a missing reflection. I even tried to use the random numbers and it was also better than doing nothing. Obviously, there is a nearly invisible line between the benefits of "filling in" missing Fobs and introducing bias. Where this line goes - is the subject of a research that to my knowledge is not done yet. Anyway, this is why phenix.refine writes out "regular" and "filled" maps: one is to give you unbiased but eventually lower quality map, and the other one is to give you a better-looking map with a risk of being biased. This way users have more options in exploring their maps (and less reasons for saying that Refmac produces better-appearing maps than phenix.refine -- see below). I have to mention that to my knowledge REFMAC always writes "filled" maps (those with missing Fobs substituted by DFc): - it is mentioned in Maria Turkenburg's thesis: http://www.ysbl.york.ac.uk/~mgwt/thesis-tth/chapter2.html#tth_sEc2.6.5 - and in Refmac docs: http://www.ccp4.ac.uk/html/refmac5/keywords/xray-general.html "Missing Data: For those reflections where the FP are missing, mFo is set equal to dFc. (...)". Correct me if I'm missing something. Please let me know if I wasn't clear in my attempt to explain this. I will update the phenix.refine documentation accordingly. Pavel.

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the different between 2mFo-DFc and mFo-DFc map
by 丁玮 30 Jun '09

30 Jun '09

hi,everybody, By phenix.refine outputde two likelihood-weighted maps: 2mFo-DFc and mFo-DFc.When they were displayed in coot, There is a vast difference between them, why? Thanks dream830106 　　　　　　　　dingding830106(a)sina.com 　　　　　　　　　　2009-06-30

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