- phenixbb - phenix-online.org

Re: [phenixbb] Autobuild error
by youssef ben ammar 06 Aug '09

06 Aug '09

Thanks for your quick reply, I tried again to fix the problem as suggested by Thomas but this did not solve the problem. Actually I have two machines running phenix, one with the old version 1.3, and the other with 1.4-3 version. With the old version I have also coot, ccp4, and arp-warp, and all things are running without any problem in this machine. But in the other computer, I don't have arp-warp in it (ccp4 and coot exist also), and everything was running OK until I updated phenix to 1.4-3. But now even if I downgrade it to 1.3, autobuild does not work. If I compare echo $PATH results from both machines, I can notice that the path in the one with "defected" autobuild is too long. I will review again my path and try to fix it, or see if there are other recently-installed programs that interfere with phenix. Thanks Youssef.

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Autobuild error -
by Gino Cingolani 06 Aug '09

06 Aug '09

Dear Youssef and Tom, I had the same problem. I also emailed the Phenix classified and got a similar response from Tom. In reality, Tom suggestion didn't solve my problem. The funny thing is that in my case PHENIX.Autobuild worked fine for months before suddenly giving the 'Word too long' error. Weird!!! Believe it or not, the only thing I had to do to fix the problem was to uninstall the ARP/wARP package (sorry about that Tassos!). I realized that PHENIX.Autobuilt stopped working properly right when I installed ARP/wARP. I guess there may be a conflict between the two programs (could Phenix read some ARP/wARP library in the wrong directory?), or something like that. I'm not sure. I'm not claiming this is a general solution, but it worked in my case. I hope it will help you! Cheers, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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Re: [phenixbb] Autobuild error
by Thomas C. Terwilliger 05 Aug '09

05 Aug '09

Hi Youssef, I'm sorry for the trouble! If you update to a recent "nightly build" such as 1.4-129 then this should go away. If it still doesn't, then have a look at your path: echo $PATH which is probably quite long....and identify a few things (perhaps ccp4 and coot for example) that you don't need while running phenix...and then add the keyword: remove_path_word_list="coot ccp4" All the best, Tom T remove_path_word_list = None .help = "List of words identifying paths to remove from PATH " "These can be used to shorten your PATH. For example..." "cns ccp4 coot would remove all paths containing these " "words except those also containing phenix. Capitalization" "is ignored." ">> Dear all, >> >> Recently I have problem with Autobuild. The process fails with the >> following >> message: >> Failed to carry out AutoBuild_build_cycle: >> child process stderr output: >> command: 'csh /home/phenix/p21/AutoBuild_run_1_/TEMP0/RUN_FILE_1' >> Word too long. >> Even if I set the path only to things related to phenix, the process fails >> with the same error. >> >> Any idea? >> >> Youssef >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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Autobuild error
by youssef ben ammar 05 Aug '09

05 Aug '09

Dear all, Recently I have problem with Autobuild. The process fails with the following message: Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /home/phenix/p21/AutoBuild_run_1_/TEMP0/RUN_FILE_1' Word too long. Even if I set the path only to things related to phenix, the process fails with the same error. Any idea? Youssef

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Using phenix.pdbtools to strip multiple conformations out of a PDB file?
by Stephen Graham 04 Aug '09

04 Aug '09

Dear all, Apologies if this is a dumb question, but I couldn't find the answer in the docs or by asking the googlebrain. Is there a simple way in phenix.pdbtools to strip "alternate conformations" of side chains, etc, from an input PDB file? By removing "alternate conformations" I mean I would like to keep the conformation with the highest occupancy (not necessarily denoted 'A' in the altLoc column) unless all conformations have an equal occupancy, in which case I'd arbitrarily keep conformation 'A'. I think it should be possible by a clever atom_selection command, but the correct syntax has thus-far eluded me! Thanks, Stephen -- Dr Stephen Graham Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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Is the twin refine conflict with order_solvent refine
by shi jiahai 04 Aug '09

04 Aug '09

Hi, Dear all, I am refine a twin dataset with phenix 1.4-3 and CCI (2008_02_08_1610) on a CenOS 5.2 workstation. When I run refine with twin law or order_solvent alone, the refinement is good. Everything goes smoothly. However if I enable refinement on both twin law and order_solvent, the error comes during the order_solvent refinement as below. Start model: number = 55 b_iso_min = 5.52 (limit = 1.00) b_iso_max = 60.32 (limit = 60.00) b_iso_mean = 24.19 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 2.13 (limit = 1.80) dist_sol_mol_max = 4.38 (limit = 6.00) Traceback (most recent call last): File "/Application/CCI/cci_apps_sources/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 80, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1162, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 350, in refinement_machine log = log) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 132, in __init__ map_cutoff = self.params.primary_map_cutoff).peaks_mapped() File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 324, in find_peaks log = self.log) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/find_peaks.py", line 65, in __init__ symmetry_flags = maptbx.use_space_group_symmetry) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 2238, in electron_density_map w2 = w2).fft_map( File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 2126, in map_coefficients "m_gradient" AssertionError Can anybody help me with this? Thanks a lot in advance! Best Regards, Shi Jiahai Department of Biological Sciences, National University of Singapore

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Assertion error while adding water
by Bishal Kumar Singh 03 Aug '09

03 Aug '09

Hi, Following error is showing while adding water. Every command-line is as default except "ordered_solvent = True". I will appreciate your suggestions. "0.7 1.17367178905 0.7 1.2044634853 0.7 1.18455476555 0.7 1.21102571346 0.7 1.20890773595 0.7 1.23028004675 0.7 1.2017635385 0.7 1.2151128962 0.7 1.20672093638 0.7 1.17881942233 0.7 1.21258440895 0.7 1.21100112067 0.7 1.22101928156 0.7 1.20955876073 0.7 1.17722437184 0.7 1.19891104532 0.7 1.18433797592 Traceback (most recent call last): File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.py", line 16, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1121, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 394, in refinement_machine log = log) File "/wrkhuge/cci_apps/cci_apps_sources/mmtbx/solvent/ordered_solvent.py", line 159, in __init__ use_kick_map = self.params.use_kick_maps).peaks_mapped() File "/wrkhuge/cci_apps/cci_apps_sources/mmtbx/solvent/ordered_solvent.py", line 334, in find_peaks log = self.log) File "/wrkhuge/cci_apps/cci_apps_sources/mmtbx/find_peaks.py", line 93, in __init__ crystal_gridding_tags = fft_map.tags() File "/wrkhuge/cci_apps/cci_apps_sources/cctbx/maptbx/__init__.py", line 152, in tags return crystal_gridding_tags(self) File "/wrkhuge/cci_apps/cci_apps_sources/cctbx/maptbx/__init__.py", line 158, in __init__ assert gridding.symmetry_flags() is not None" regards, Bishal Singh

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Autosol error
by Francis E Reyes 01 Aug '09

01 Aug '09

All When issuing phenix.autosol native.data=scala_072809B_3_001.mtz deriv.data=scala_072909A_3_001.mtz deriv.atom_type=Ir deriv.sites=5 deriv.inano=noinano native.labels='IMEAN SIGIMEAN' deriv.labels='IMEAN SIGIMEAN' I get the error **************************************** AutoSol Input failed For SIR datasets please enter two datafiles or datasets.(native +deriv) Please treat MIR as a series of SIR datasets ...to specify a particular set of data you can specify one of the following (command-line format shown, for a script take out the '=' and use the keyword 'group_labels_list' instead): native.labels='IMEAN SIGIMEAN' deriv.labels='IMEAN SIGIMEAN' native.labels='I(+) SIGI(+) I(-) SIGI(-)' deriv.labels='I(+) SIGI(+) I(-) SIGI(-)' **************************************** Any ideas? thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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combining models from multi-start simulated annealing
by James Whittle 30 Jul '09

30 Jul '09

Is there a way to use AutoBuild to combine a set of models created by multi-start simulated annealing? I've used a random number generator to seed different SA runs at two temperatures, as suggested on this bulletin board before ... but can combine the best parts of these models automatically? --James

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Integrating Phenix with Torque
by Jeremy Mann 29 Jul '09

29 Jul '09

A new user of mine wants to run Phenix on two of our clusters. We use Torque/Maui as our batch scheduler and would like to integrated their usage of Phenix. They want to run something like: phenix.autobuild data=data.hkl seq_file=seq.dat model=model.pdb multiple_models=True multiple_models_number=20 n_cycle_rebuild_max=5 nbatch=20 nproc=20 The documentation mentions briefly the ability to use batch schedulers but doesn't give examples of submission scripts. -- Jeremy Mann jeremy(a)biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672

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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 25 Jul '09

25 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 25 Jul '09

25 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 22 Jul '09

22 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] 18 Jul '09

18 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 17 Jul '09

17 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 17 Jul '09

17 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 16 Jul '09

16 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 16 Jul '09

16 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 15 Jul '09

15 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 11 Jul '09

11 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 10 Jul '09

10 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

1 0

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

2 1

GUI problems
by Phil Evans 02 Jul '09

02 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.

1 0

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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Autobuild requires more then 24 hrs to run on 32 cpu?
by Tatyana Sysoeva 30 Jun '09

30 Jun '09

Hello! I am trying to use Autobuild wizard and it seems that it takes longer time that I expected. That's why I have next questions: 1. What is "usual" time range estimate for Autobuild run with default parameters if my model has 7 chains with 284 aa in each? (if I'm running Autobuild on a single machine it does not finish in 3 days or on cluster with usage of 32 processors - in 24 hours) 2. Do I use phenix comman correctly for using several machines at once? I used /phenix-1.4-89, command line *phenix.autobuild data=e239a.hkl seq_file=seq.dat model=model.pdb nproc=32* In 24 hrs, which is my limit on cluster time, I get next things - AutoBuild_run_1_1_/AutoBuild_run_1_1.log ends with *Setting up to build 5 models to be combined into final model #1 NOTE: input model will be rebuilt in place: nothing will be added or deleted. Building 5 models ... Running up to 32 jobs in parallel... Splitting work into 5 jobs and running 32 at a time with csh in /home2/tas354/phenix_runs/20090610/1/AutoBuild_run_1_/TEMP0 Starting job 1... Starting job 2... Starting job 3... Starting job 4... Starting job 5...* AutoBuild_run_1_1_/TEMP0/AutoBuild_run_1_N.log ends with *Copying refined_pdb_in.pdb to composite_model.pdb in AutoBuild_run_1_/TEMP0 Beginning merge with current best model: refined_pdb_in.pdb Merging models: composite_model.pdb refine_1.pdb Refining model: Build_composite_3.pdb Model: AutoBuild_run_1_/TEMP0/Build_composite_refined_3.pdb R/Rfree=0.23/0.25 Rebuilding side chains from Build_composite_refined_3.pdb* or with error * TRIED resolve_extra_huge ...but not OK ******************************************************************************** Failed to carry out AutoBuild_build_cycle: ******************************************************************************** * Should I change parameters of the Autobuild which will dramatically reduce time for computations or should I ask for extension of my time for letting the programs to run as it is? I would give more details if it is needed I just could not think of some other right now. And I would appreciate any advices and suggestions! Thank you Tanya

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phenix.refine simulated annealing modes
by Alejandro Buschiazzo 30 Jun '09

30 Jun '09

Dear Phenix users, I can't find information on the precise meaning of the different modes to perform SA during refinement; some choices are self-explanatory (such as "every_macro_cycle" or "second_and_before_last"), but what about "once" or "first_half"? (in my particular case, I want to perform only one simulated annealing routine on the second macro_cycle: can I use "once"? but, where should I define at which cycle to perform it?) Thank you for your help, Best, -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185

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questoin about AutoBuild
by crystallogrphy 28 Jun '09

28 Jun '09

Deal All, After I tried 9 runs of AutoSol from my MAD data by changing parameters (resolution, heavy atom numbers), I got 9 results, named as: AutoSol_run_1_ to AutoSol_run_9_. I found #9 and #7 have the lowest Rfree, so I want to pick the model from these two runs. However, when I use "phenix.autobuild after_autosol", the resulting AutoBuild files tell me that the program picked the result from #5 of AutoSol, not the lastest #9. Does anyone know how can I specify the exact number of AutoSol to run autobuild? I also tried this command "phenix.autobuild data=resolve_3.mtz model=overall_best.pdb seq_file=zntb-sd.seq"under the directory of AutoSol_run_9_, but failed with the following word: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_2_/TEMP0/NO_LIG_NO_WAT_overall_best_edited.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting... See AutoBuild_run_2_/LAST.LOG for more information Please resolve the R-free flags mismatch. ******************************************************************************** Does anyone know where is wrong? 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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"phenix.fobs_minus_fobs_map" new tool in PHENIX
by Pavel Afonine 28 Jun '09

28 Jun '09

Hi Everyone, for all of you who asked about computing Fo-Fo map in PHENIX: I added a new command line tool called "phenix.fobs_minus_fobs_map". For usage details just type phenix.fobs_minus_fobs_map and hit Enter, and it will print a couple of examples. Any feedback will be very appreciated. This is available in development version of PHENIX starting from 1.4-51: goto: http://www.phenix-online.org/download/ then click "Latest installers" under "Nightly builds (version 1.4-4 and above)" section. Pavel.

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Refining partially occupied DNA on top of itself
by bschmidt＠berkeley.edu 27 Jun '09

27 Jun '09

Hello, I am having difficulty using Phenix to build and refine a DNA duplex. The issue is that my asymmetric unit consists of one protein monomer bound to DNA, but the protein is a dimer and the DNA is not palindromic, so each monomer is bound to a different sequence of DNA. As such, the density for the two different DNA half-sites is averaged out in the asymmetric unit. I have tried to place two duplexes directly on top of one another, each with 0.5 occupancy, and then refine. But I have noticed two problems. The first is that when xyz refinement is off, and I look at the output files, the density for DNA is awfully green, as if there were only *one* helix with 0.5 occupancy there. The other problem I noticed is that when I turn xyz refinement on, and look at the output files, one of the two half-sites gets moved several angtroms, so that it is in a region that generally has no density. I expect that, if done properly, the backbone of both half-site DNAs ought not to move. Any advice would be greatly appreciated. Thanks, Bryan Schmidt

4 7

multi-xtal averaging vs twinning
by Frank von Delft 26 Jun '09

26 Jun '09

Hi, I'm trying to to figure out how to transfer phases from a twinned SeMet dataset to the native one for refinement. 1) SeMet dataset (2.9A) is solved (despite twinning), structure built, refines 29/35 (ish) 2) SeMet crystals are hemihedrally twinned (confirmed by refining with twin law), native probably too. 3) Native dataset (2.7A) has 5A difference in the long cell edge (478 vs 483A). So I could (and will try to) simply copy the SeMet phases into the native dataset, even though CC Fnat and Fsme is rather low (80-20%). But would phenix.multi_crystal_average know what to do with this? It has no explicit options, so I expected not. Or how *would* one approach this? Cheers Frank

4 7

Fix for autobuild/ligandfit problem with long $PATH
by Tom Terwilliger 25 Jun '09

25 Jun '09

Hi Phenix users, Several of you have had trouble with phenix.autobuild (or phenix.ligandfit) failing if you had a very long $PATH. The problem seems to be that if your $PATH is very long, then adding more to it and re-setting it can lead to a string that is too long (on some systems). Starting with PHENIX version 1.4-100 (today's version) you can add the keyword remove_path_word_list=" cns xiaroot ccp4 phaser" to shorten your $PATH. This keyword will selectively remove all paths from $PATH that include any of the words you specify, and that do not include the word "phenix", when running that phenix job. The log file will list what paths were removed. To figure out what paths to remove, type echo $PATH and choose the ones that identify other programs that are not part of phenix. I hope that will do it! Please let me know if this doesn't solve the problems. All the best, Tom T 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

1 0

How to apply geometry regularization to selected residues in phenix.pdbtools
by Oliv Eidam 25 Jun '09

25 Jun '09

Hi, I was wondering if the geometry regularization in phenix.pdbtools can be applied to selected residues only. Something like: > phenix.pdbtools my.pdb selection="resname xyz" --geometry-regularization Many thanks in advance, Oliv -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: eidamo(a)blur.compbio.ucsf.edu

3 2

pseudo translational symmetry
by youssef ben ammar 23 Jun '09

23 Jun '09

Hi all, I recently solved the structure of a protein containing 395aa using phenix autosol. After autoBuild I got about 65% of the sequence docked with 2 monomers in the ASU. After several refinement cycles the map has been improved and I build manually the remaining amino acids. But the problem is that R and Rfree didn't decrease below 0.28 and 0.33 respectively. I tried with NCS restraints, TLS but without success. When I revised phenix autosol logs carefully, I found that in xtriage the analyses of the Patterson function reveals a significant off-origin peak that is 41.59 % of the origin peak, indicating pseudo translational symmetry and no twin laws were found. The space group is P212121 (36.898, 59.45, 393.908, 90, 90, 90). The basic statistics suggested 1 copy in the ASU (but the solution gave 2 copies per ASU !!!). The same analysis done by ccp4i gave the same solvent content and math. coef. in p21212 but with 2 copies per ASU. In xtriage I found this suggestion: If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space group P 21 21 2 (b-1/4,2*c,a) operator x, y+1/2, z unit cell of reference setting (393.91, 36.90, 29.73, 90.00, 90.00, 90.00) I am really stucked with the refinement and don't know how to deal with this pseudo translation. Any help or suggestions are welcome. Thank you. Youssef

3 2

density fit analysis in coot
by Raja Dey 23 Jun '09

23 Jun '09

Dear Friends, Can anyone tell what the number popping up against every bar of the density fit analysis histogram in COOT is? Is it a correlation co-eff between Fo and Fc or something else? I am interested to know how is this parameter calculated. One more question... Is it possible to build a model in COOT if only the electron density map and sequence is given? Although I know there are some programs to create an initial model. I am wondering whether COOT can do that. Thanking you in advance... Raja

2 1

error loading SHELXL HKLF4 reflection file
by jonathan elegheert 22 Jun '09

22 Jun '09

Dear phenix developers, I am using the one of the latest phenix.refine nightly builds, and I'm trying to load a SHELXL .hkl file into phenix; phenix.refine xxx_refine_004.def xray_data.file_name="/path/xxx.hkl"=hklf4 The "Iobs,SigIobs"labels are well recognized (so the "Merging symmetry-equivalent intensities" subroutine works ok), but the necessary "=hklf4" or "=intensities" appendage seems to cause problems. The strange thing is that in phenix.xtriage, the same command line flag works perfectly fine. Thank you for any pointers! Jonathan Elegheert PhD student Ghent University -------------- Traceback (most recent call last): File "/usr/local/phenix-1.4-95/phenix/phenix/command_line/refine.py", line 19, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 245, in __init__ log = self.log) File "/usr/local/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 201, in __init__ self.raw_flags = self.extract_flags(data = self.raw_data) File "/usr/local/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 266, in extract_flags parameter_scope = self.flags_parameter_scope) File "/usr/local/phenix-1.4-95/cctbx_project/iotbx/reflection_file_utils.py", line 566, in get_r_free_flags miller_arrays = self.get_miller_arrays(file_name=file_name) File "/usr/local/phenix-1.4-95/cctbx_project/iotbx/reflection_file_utils.py", line 406, in get_miller_arrays if (os.path.samefile(canonical_file_name, tabulated_file_name)): File "/usr/local/phenix-1.4-95/build/intel-linux-2.6-x86_64/base/lib/python2.6/posixpath.py", line 153, in samefile s2 = os.stat(f2) OSError: [Errno 2] No such file or directory: '/path/xxx.hkl=hklf4'

2 1

Re: [phenixbb] scaling
by Thomas C. Terwilliger 20 Jun '09

20 Jun '09

Hi, You can use autosol to do scaling of any pair of datasets, so if you just run the command below N times, once for each reference/to-be-scaled dataset pair you are interested in, it should do what you want: phenix.autosol native.data=native.sca deriv.data=deriv.sca correct_aniso=false skip_xtriage=true res_hyss=100 build=false this will stop with " HYSS failed...Probably no iso or ano differences.." because we are not giving HYSS any data. Then the file: AutoSol_run_1_/TEMP0/AutoSol_run_1_/TEMP0/mir_fbar.mtz will have the scaled native and deriv data in mtz format. For subsequent runs, the data will be in AutoSol_run_2_ ...etc I hope that helps! -Tom T >>> where ought i look for a phenx utility to scale any number of data sets >>> to >>> a reference data set? something akin to scale.inp in CNS. >> >> I don't think we have such a utility, unless there is something in >> solve (Tom?). -- But you shouldn't need this for any of the phenix >> applications. All trivial scaling of the scale.inp type is done >> on-the-fly. >> Ralf >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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scaling
by Bryan W. Lepore 20 Jun '09

20 Jun '09

where ought i look for a phenx utility to scale any number of data sets to a reference data set? something akin to scale.inp in CNS. -bryan

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