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error on Autobuild GUI on new version (1.7.629)
by Young-Jin Cho 07 Jan '11

07 Jan '11

Hi Phenix developers, I recently installed new version of phenix(phenix-1.7-629) FYI. I chose this installer version phenix-installer-1.7-629-intel-linux-2.6-x86_64-fc3.tar as my computer indicates 2.6.18-194.17.4.el5 x86_64 after uname -rm command. Everything was ok until I started AutoBuild program. Somehow it keeps giving me following error messages on my GUI window: ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /amnt/datnew/yjcho/RUN_FILE_2.log : ImportError: numpy.core.multiarray failed to import Possibly this subprocess is run on a machine with different architecture than the main process? ******************************************************************************** *************ERROR ENDING ******************* I would thank if you can help me out from this problem. Thanks in advance, Young-Jin

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anisotropic refinement gui more than one chain
by Christian Roth 06 Jan '11

06 Jan '11

Dear all, I want refine a structure with several chlorides and want refine these chlorides anisotropic. I use the GUI for the setup and manipulate the eff file just before it starts. To my surprise my constrained group definitions are used, but my anistropic refinement definitions are removed I incorporated it as followed: adp { individual { isotropic = None anisotropic = "chain a" anisotropic = "chain f" anisotropic = "chain Y" anisotropic = "chain T" anisotropic = "chain U" anisotropic = "chain z" anisotropic = "chain d" anisotropic = "chain g" anisotropic = "chain e" anisotropic = "chain V" anisotropic = "chain X" anisotropic = "chain n" } but in the log the following is stated: adp { individual { anisotropic = "chain a" } Why are all the other definitions gone? And if I defined it wrong, how I have to define it correctly? The current version I use is 1.6.4-486 Thanks Christian

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CCP4 SW Web Broadcast
by ronan.keegan＠stfc.ac.uk 06 Jan '11

06 Jan '11

Dear All, For those of you hoping to view the CCP4 Study Weekend online, we're experiencing some technical difficulties with the webcast equipment. Unfortunately the live stream won't be available for the first part of the meeting. We're hoping to fix it as soon as possible and we'll send an update as soon as it's available. Our apologies for the inconvenience. Best wishes, Ronan Ronan Keegan CCP4 Group -- Scanned by iCritical.

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Questions about phenix.refine with twin_law
by Keitaro Yamashita 06 Jan '11

06 Jan '11

Dear Phenix developers, I'm working with pseudo-merohedrally twinned data (fraction 45%), using Phenix-dev-616. I have three questions about phenix.refine with twin_law. (running on the command line) During refinement with twin_law, the log file says x-ray target function is set to "twin_lsq_f". Does it mean, we cannot use maximum likelihood target for twinned data? If so, is it recommended to refine without twin_law at first several cycles? When I tried to refine using the model refined without twin_law, the target function was still ml, not twin_lsq_f although I specified twin_law. Is this a bug? When I used twin_law option, in the table "R-free likelihood based estimates", "Scale factor" were None in all resolution bins. Cannot scale factor be calculated during twin refinement? Thanks in advance and Wishing you the best holidays, Keitaro

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How to get a statistics of sidechain&mainchain Bfactors?
by 商元 05 Jan '11

05 Jan '11

Dear all, I used TLS+ADP refinement to get the final structure model, after that I used phenix.model_vs_data to get the statistics for table1. However there is no B factor statistics in the output. Can I get the overall B factor by just simply averaging the B factors of each residue in the output text? Then how can I get the B factor value of the sidechains and that of the mainchain? Thanks and regards, Yuan SHANG Hong Kong

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DNA covalent bond angles deviate from PDB standard dictionary
by Scott Classen 05 Jan '11

05 Jan '11

Hello, I'm running into validation problems with DNA when validating on PDB website. the validation report indicates that the refined value is significantly different that the PDBs standard dictionary. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Standard Name ID Number Angle Value Deviation ------------------------------------------------------------------------------------------- 2.2 DG D 6 N9 - C1' - O4' 110.5 108.3 0.3 2.6 DC D 7 N1 - C1' - O4' 110.9 108.3 0.3 2.3 DC D 8 N1 - C1' - O4' 110.6 108.3 0.3 3.0 DT D 9 N1 - C1' - O4' 111.3 108.3 0.3 I've looked through a few of these in the .geo file and it appears that phenix.refine is using different values. for example, angle pdb=" O4' DG D 6 " pdb=" C1' DG D 6 " pdb=" N9 DG D 6 " ideal model delta sigma weight residual 108.40 110.18 -1.78 3.00e+00 1.11e-01 3.52e-01 ideal is specified as 108.4º so clearly my refinement has converged, but it has NOT converged on the RCSBs accepted value of 110.5º What to do? Who is "right" phenix or RCSB? Thanks, Scott

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bugs in dev 625
by Weiergräber, Oliver H. 05 Jan '11

05 Jan '11

Hello, trying to use phenix.autobuild (command line version, didn't try the gui) in dev 625, I encountered the following error: ############################################ Build cycle 1 of 6 method:rebuild Initial rebuild cycle: just combining previous models or copying over initial PDB file Using edited_pdb.pdb for rebuild, copied to unrefined.pdb_1 Refining model: unrefined.pdb_1 No refinement carried out (may need free R flags) Error message from phenix.refine: global name 'libtbx' is not defined Refinement failed... ############################################ If invoked directly, phenix.refine seems to run fine, so there may be a problem with scripting in the autobuild wizard. Regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institut für Strukturbiologie und Biophysik ISB-3: Strukturbiochemie Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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viewing maps in xfit
by David Shin 04 Jan '11

04 Jan '11

Hi - Anyone have a script to convert phenix .mtz output so I can read in maps in xfit? I still find xfit handy for a few things. D

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errors when disabling Rfree
by chene＠umbi.umd.edu 02 Jan '11

02 Jan '11

Dear Phenixers, I have a low resolution twinned data, for which I disabled cross validation in refinement. The refinement worked and exported the refined coordinates. However, the phs files for maps are empty and there were such errors as below. It seems the free set is required for maps. I wonder how to fix this problem? Thanks Chen Traceback (most recent call last): File "/home/chene/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 103, in run map_manger.write_files() File "/home/chene/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1281, in write_files fmodel = self.refine_object.fmodels.fmodel_xray(), params = mtz_mc) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/maps/__init__.py", line 290, in map_coefficients_from_fmodel centrics_pre_scale = params.centrics_pre_scale) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1780, in map_coefficients w2 = w2) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1695, in map_coefficients sigmaa_object = self.sigmaa_object( detwinned_data=dt_f_obs,f_model_data=tmp_f_model, tmp_free=tmp_free,forced_update=True) File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1504, in sigmaa_object kernel_width_free_reflections=200, File "/home/chene/phenix-1.6.4-486/cctbx_project/mmtbx/scaling/sigmaa_estimation.py", line 131, in __init__ raise RuntimeError("No free reflections.") RuntimeError: No free reflections. Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

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Automated Mg & K ions picking
by Hasan Demirci 02 Jan '11

02 Jan '11

Hi, I have a low resolution data and I am trying to place Mg++ and K+ ions. As far as I know for ligand search at least 3 atoms required. Is it possible to do an automated search of these single atom ions by using phenix similar to automated water picking protocol? Thanks. -- Hasan DeMirci, Ph.D. Postdoctoral Fellow Department of Molecular Biology, Cellular Biology & Biochemistry Brown University 185 Meeting Street Providence, RI 02912 (401) 863-3652 lab (SFH) (401) 863-6124 lab (ship st) (401) 226-7852 cell Hasan_DeMirci(a)Brown.edu demircha99(a)gmail.com

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