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Phaser RMS - What happens when it is too high
by Peter Grey 29 Jul '09

29 Jul '09

Hi all, In Phaser RMS is a crucial parameter. I had several cases where underestimation of RMS resulted in negative LLG. The cure was simply increasing the RMS. But I wonder, are there negative effects to a too high RMS. What are the dangers of giving Phaser a too high RMS ? Are there any indications in the output for that. This is also important with EM maps as models since in that case estimation of RMS is difficult. Many thanks in advance for your advice and insight, Peter.

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phenix.refine issue
by Dennis Wolan 28 Jul '09

28 Jul '09

I am having an issue with running a simple phenix.refine that I have never encountered before. I get a list of issues and the program quits with: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/ refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 231, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 566, in reflection_file_server err=self.log) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in as_miller_arrays and flex.min(column_group.sigmas()) > 0): RuntimeError: min() argument is an empty array I have no idea if the issue is with my pdb or mtz. I'm sure it's something very simple that I just am not identifying. Thanks in advance, Dennis

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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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