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optimize_wxc won't run
by Nian Huang 29 Apr '08

29 Apr '08

Dear All, I am a novel phenix user. There is a problem whenever I use option optimize_wxc in phenix. The error message looks like following, ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' I don't know what's the problem. Could it be my installation? Nian Huang, Ph.D. Dept. of Biochemsitry UT Southwestern Medical Center

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"gnomebreakpad": libgnomebreakpad.so: error
by shivesh kumar 23 Apr '08

23 Apr '08

Dear all, We are using Fefora core 8. To start phenix, we give the command phenix in the terminal, after 30-40 minutes it shows the following error message *Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory and after 1hr of this message the GUI comes.There is no problem in running phenix afterwards and also with any other programs like CCP4, CNS etc... I have put this query earlier also and I got reply as follows yum install bug-buddy It didn't work for us.If anyone can suggest the solution, it would be very helpful for us.Thanx in advance. shivesh *

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twinning analysis
by Andreas Förster 23 Apr '08

23 Apr '08

Hey all, I've been digging around with a nasty dataset for a while, twinning, pseudosymmetry, etc. Phenix.xtriage has helped me make some guesses as to what's going on, but phenix.twin_map_utils fails. I used an mtz file obtained from XDS via f2mtz and cad as xray data, like so: phenix.twin_map_utils xray_data.file=blah.mtz model=blah.pdb unit_cell=86.623,86.623,121.357,90,90,120 space_group=P65 Here's the error: Traceback (most recent call last): File "/usr/local/2008_02_08_1610/cci_apps_sources/mmtbx/mmtbx/command_line/twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/usr/local/2008_02_08_1610/cci_apps_sources/mmtbx/mmtbx/twinning/twin_map_utils.py", line 256, in run tmp_params = utils.r_free_flags_params.extract() AttributeError: 'module' object has no attribute 'r_free_flags_params' I see the error on a recent macbook pro with current cci_apps. How can I get around it? Thanks Andreas ps. I apologize if that question posted to the board earlier. I wrote from a wrong account.

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NCS problem
by Bobby Huether 22 Apr '08

22 Apr '08

Hello, My structure contains 2 protein molecules in the asymmetric unit, and they are related by 2-fold rotational NCS to form a dimer. The refinement is nearing completion (1.7 A) and the solvent molecules are now being included. A blob of density has been tentatively identified as being occupied by glycerol, which was present as the cryo-protectant. The issue is that this blob of density lies on the 2-fold NCS rotation axis, and so we need to use 2 glycerol molecules within this density, each at 0.5 occupancy, to conform to the NCS symmetry. This blob of density lies in a surface pocket formed by residues from both NCS-related proteins. When we build in the 2 glycerol molecules and then use phenix.refine, the two glycerols are pushed out of density. Presumably this is because phenix.refine is interpreting this situation as two glycerol molecules sitting on top of on another rather than interpreting it as being a model for a disordered ligand. Can phenix.refine handle this situation? Thanks, Robert

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Omit map around a ligand
by mathieu Coincon 22 Apr '08

22 Apr '08

Hi, I tried to use phenix.autobuild to generate a SA-omit map around a non-protein residue but I didn't succeed. Can someone give me a recipe? (perhaps with file from the ligand fit examples.... ;-) ) Thanks. Have a nice day. Mathieu. ____________ Mathieu Coinçon Biochemistry PhD Student Université de Montréal (+1)514-343-6111 #5352

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Re: [phenixbb] Phenix on Altix 350 ?
by Sankar Narayanan Manicka 21 Apr '08

21 Apr '08

Dear Sir, Sorry for the delay. It was a long weekend here. the output of /etc/*release SUSE LINUX Enterprise Server 9 (ia64) VERSION = 9 PATCHLEVEL = 3 SGI ProPack 4SP3 for Linux, Build 403r1-0512182217 sincerely sankar Ralf W. Grosse-Kunstleve wrote: >> Yes, I could install the CCI_apps Source without any problem. And i ran >> the file "test_apps" without any problem. >> > > Great! > Chances are the next full Phenix source installer will also work. > > If you get a chance, could you send the output of > > cat /etc/*release > > uname -a > > boost_adaptbx.show_platform_info > > Thanks! > Ralf > > > -- ****************************************************************** Sankar N. Manicka C/o Prof. S. Krishnaswamy Dept. of Genetic engineering School of Biotechnology Madurai Kamaraj University Madurai 625 021 TN INDIA mailto: sankar(a)mkustrbioinfo.com ******************************************************************

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random seed to phenix.reflection_file_converter
by iulek＠interponta.com.br 19 Apr '08

19 Apr '08

Hi, Is there a way to provide a random seed to "phenix.reflection_file_converter" such that two runs will produce the same result (the same reflection set flagged as free)? What would be the syntax? For while I could only find for the context of refinement and simulated annealing ... Thanks, Jorge

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questions about twinned structure and MR
by Christina Bourne 18 Apr '08

18 Apr '08

Hello bb, I am new to Phenix and am facing my first twinned structure. While I wait for my copy of Yeates Methods in Enzymology (albeit from 1997) to be delivered, perhaps this bb could answer a few questions? At what point do I detwin, or do I not do it at all? It seems Phenix does this itself, on the fly? Is it refining the twin fraction too? MR (Phaser) finds solutions with twinned or detwinned data. However, the solutions vary by 180degrees, so I suspect I'm finding solutions for both h,k,l and h,-k,-l. These come from two different runs, but one has refined LLgain of 1010.8 (matches soln found with detwinned data, both run through ccp4), and other has refined LLgain of 1073 (through Phenix; it's rotated 180degrees from the other). When performing AutoBuild after AutoMR, should I worry that I haven't assigned Rfree? Does Phenix account for twinning when it does this automatically, or what keyword(s) do I need to include? I see a section in the documentation about refining twinned structures, and am looking forward to getting to that point! I just want to be sure I'm following a "correct" procedure for the steps leading up to that. From the literature, it seems quite common to not account for twinning until refinement. My concern is the two MR solns...which should I use? If I know it's twinned, shouldn't I account for that from the beginning? More details: P41, data good to 2.2A, 2 molecules in the AU, twinning fraction ~0.4. Rmerge from scaling is reasonable at ~11% overall. MR model is 100% identical to this data, but from a different spacegroup (thus I'm running MR). Thanks for any tips or guidance! Christina Bourne ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Phenix on Altix 350 ?
by Sankar Narayanan Manicka 16 Apr '08

16 Apr '08

Sir, I would like to install Phenix on an SGI Altix 350 server with five 64 bit intel itanium processors. How do i proceed ? sincerely sankar -- ****************************************************************** Sankar N. Manicka C/o Prof. S. Krishnaswamy Dept. of Genetic engineering School of Biotechnology Madurai Kamaraj University Madurai 625 021 TN INDIA mailto: sankar(a)mkustrbioinfo.com ******************************************************************

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how to avoid self disulfide bond in phenix refinement?
by Chen Chen 14 Apr '08

14 Apr '08

Hi, I am having a problem in phenix.refine. I ran phenix.refine --dry_run foo.mtz foo.pdb The program generate a parameter file named foo.param. I made some modification of foo.param. Then ran phenix.refine foo.mtz foo.pdb foo.param The program reports a weir error message: ========================== Set up restraints manager ========================== Number of disulfides: simple=3, symmetry=0 Simple disulfide: " SG CYS A 29 " segID="A " - " SG CYS A 29 " segID="A " distance=0.00 Simple disulfide: " SG CYS A 180 " segID="A " - " SG CYS A 180 " segID="A " distance=0.00 Simple disulfide: " SG CYS A 286 " segID="A " - " SG CYS A 286 " segID="A " distance=0.00 ... Sorry: Bond restraint model distance < 0.001: Please inspect the output above and correct the input PDB file. ======================================================================== It seems that the program recognized three "self-disulfide" bonds. This problem happens even I do not make any modification in foo.param. However, if I just ran phenix.refine foo.mtz foo.pdb with every parameter at default, the programs runs OK without the above error. I am wondering if it is a bug or if I made some mistakes. Thanks Chen -- Chen Chen, Ph. D., Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 Office Phone: 240-314-6122

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