- phenixbb - phenix-online.org

Re: [phenixbb] phenix.refine 1.3 vs. 1.4 map quality ?
by William G. Scott 06 Aug '09

06 Aug '09

Hi Paul et al: The yellow map is filled and the blue map is no-fill from the phenix- generated mtz file: http://sage.ucsc.edu/~wgscott/mystuff/filled_vs_unfilled.pdf So I think this is clearly what is going on. Thanks. Bill

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Segmentation Fault
by Waight, Andrew 06 Aug '09

06 Aug '09

Hello All, I've recently solved a membrane protein structure largely with the help of phenix refine. I also have been using the autobuild programs recently for ligand fitting and whatnot. The program during this time has been running flawlessly on my machine (Ubuntu 9.04 E8400 3.0ghz etc etc) However this weekend Autobuild and AutoMR spontaneously started throwing this error. (boost_adaptbx_segmentation_fault_backtrace+0x1f) [0xb7de2e27] Segmentation fault (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 This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Memtest 86 says my RAM is good. I have reinstalled phenix and am still getting the same error. I can't seem to find any other information on this error (segmentation faults are tricky I know) and am just wondering if anyone else has seen or solved this type of problem, thanks for your help. Andrew Waight Wang Lab Skirball Institute of Biomolecular Medicine NYU school of medicine </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE>

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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 05 Aug '09

05 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 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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