March 2007 - phenixbb - phenix-online.org

freeR syntax question in phenix.refine
by Simon Newstead 20 Mar '07

20 Mar '07

Dear BB, Sorry for the obvious question, but I couldn't find a description of the syntax for the FreeR flag function in phenix.refine. Is there a paragraph on the phenix web site that explains what I should put in these fields: r_free_flags { file_name = "S19_sigmaa1.mtz" label = "FreeR_flag" test_flag_value = 0 --> don't know what this means? disable_suitability_test = False --> implications of this? I was running refinement from an mtz file from sigmaa in ccp4 with an appropriate FreeR flag designated in the MTZ file. phenix.refine worked fine and seemed to exclude the test reflections, but I wanted to know what these commands do. Cheers, Simon.

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Twinned Refinement
by Axelrod, Herbert 19 Mar '07

19 Mar '07

Hi, I was wondering if anyone has tested the new version of phenix.refine for the refinement of twinned diffraction data. Last week at Asilomar, Pavel presented a nice talk at Asilomar on the capabilities of phenix.refine to handle twinned data. Best wishes, Herbert L. Axelrod Stanford Synchrotron Radiation Lab

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phenix.refine crash
by Jianghai Zhu 19 Mar '07

19 Mar '07

Hi, I was using phenix.refine from the latest cci apps bundle to do tls +individual_sites+individual_adp refinement. The program crashed with the following error message. ----------Target weights (before refinement)---------- Traceback (most recent call last): File "/nfs/home/jzhu/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 "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ command_line.py", line 75, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ driver.py", line 1108, in run log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ strategies.py", line 245, in refinement_machine log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ weight_xray_chem.py", line 222, in __init__ compute_gradients = True) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/restraints.py", line 144, in energies_adp_aniso xray_structure = xray_structure, File "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/ __init__.py", line 109, in __init__ self.check_flags(fl_i) File "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/ __init__.py", line 177, in check_flags assert not fl.use_u_aniso() AssertionError Anyone has any idea what is happening? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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More stringent water picking
by Schubert, Carsten [PRDUS] 19 Mar '07

19 Mar '07

Hi, is it possible to increase the stringency criteria for picked waters, besides increasing the sigma level? E.G. something on the order of the H-bonding criterion found in CNS? I find that the automated water-picking routine gives me quite a few waters, which are not necessarily justified by visual inspection of the maps. Thanks Carsten

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Re: [phenixbb] More stringent water picking
by Schubert, Carsten [PRDUS] 19 Mar '07

19 Mar '07

Thanks Guys, would it be possible to implement the H-bonding criteria? From my experience with CNS it worked quite nicely. Right now I end up with ~350 waters in a 2.3 A structure of a 30kDa protein, which is a bit much. -----Original Message----- From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] Sent: Monday, March 19, 2007 1:02 PM To: PHENIX user mailing list Subject: Re: [phenixbb] More stringent water picking Hi Carsten, thanks for your question! The main water picking criteria in phenix.refine are: 1) Fo-Fc map; 2) 2Fo-Fc map; 3) macromolecule - water distance; 4) water-water distance; 5) B-factors and occupancies max/min values; plus some more of expert level ... There is no specific H-bonding criteria implemented. You can play with sigma cutoff for both maps and with the distances above. In most of the cases it the reasonable behavior. I would be interested in Paul's (Adams) comments about his experience of usefulness of H-bonding criteria in CNS. Thanks! Pavel. Schubert, Carsten [PRDUS] wrote: Hi, is it possible to increase the stringency criteria for picked waters, besides increasing the sigma level? E.G. something on the order of the H-bonding criterion found in CNS? I find that the automated water-picking routine gives me quite a few waters, which are not necessarily justified by visual inspection of the maps. Thanks Carsten _____ _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org <mailto:[email protected]> http://www.phenix-online.org/mailman/listinfo/phenixbb <http://www.phenix-online.org/mailman/listinfo/phenixbb>

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Re: [phenixbb] OS X installation problem
by Ralf W. Grosse-Kunstleve 18 Mar '07

18 Mar '07

> powerpc-apple-darwin8-g++-4.0.0 (GCC) 4.0.0 20041026 (Apple Computer, > Inc. build 4061) There is a more recent Xcode release that works here. I.e. if you still want to compile from sources, upgrade the Xcode tools. You can get them for free at Apple's developer web site. However... > is that the 10.3.9 bundle? Yes, exactly. I should also work under 10.4. I recommend trying this first. It is also most faster than a source installation (just a few seconds). Ralf

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Re: [phenixbb] OS X installation problem
by Ralf W. Grosse-Kunstleve 18 Mar '07

18 Mar '07

I have not seen this error before. Could you send me the output of c++ --version Note that we have binary bundles for PowerPC Macs. Did you try that one? Ralf

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OS X installation problem
by Arthur Glasfeld 17 Mar '07

17 Mar '07

Hi, I'm following Bill Scott's instructions for installing cci_apps on a G5 mac. I've attempted it from the self-extracting file and from the gzipped file. I type the following commands: /System/Library/Frameworks/Python.framework/Versions/Current/bin/ python ../cci_apps_sources/libtbx/configure.py phenix source setpaths.sh num_cpu=$( sysctl hw.logicalcpu | awk '{print $NF}' ) libtbx.scons -j $num_cpu . and things begin OK, but then after a bit of compiling, I get: /usr/local/cci_apps/cci_apps_sources/boost/libs/python/src/object/ inheritance.cpp:120: instantiated from here /usr/local/cci_apps/cci_apps_sources/boost/boost/graph/ graph_concepts.hpp:74: error: base 'boost::concepts::IncidenceGraph<boost::reverse_graph<boost::<unnamed>:: cast_graph, const boost::<unnamed>::cast_graph&> >' with only non- default constructor in class without a constructor scons: *** [boost/libs/python/src/object/inheritance.o] Error 1 scons: building terminated because of errors. usr+sys time: 5.92 seconds wall clock time: 37.99 seconds I had no problems in an intel mac. Anything obvious I should have done? Thanks in advance for any assistance, Arthur Arthur Glasfeld Department of Chemistry Reed College 3203 SE Woodstock Blvd. Portland, OR 97202 USA

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Re: [phenixbb] phenix.refine crash -- other error
by Peter Zwart 16 Mar '07

16 Mar '07

Good to know. Let me know if the refinement is any faster. Cheers Peter Ulrich Baumann wrote: > Yop, that did it --- I sourced an old phenix setpaths and not the cci_apps. > > Thanks a lot, > > Ulrich > > Quoting Peter Zwart <PHZwart(a)lbl.gov>: > >> Hi Ulrich, >> >> Please make sure that the phenix.python used is actually the >> phenix.python you installed with cci_apps. >> >> The behavoir seen might be due to using an other phenix.python >> installation (on that loads in old python libraries). This can be >> avoided by making sure that the last crystallographic package sourced in >> your .chsrc file, is the latest phenix/cci_apps installation. >> >> A which phenix.python might give a clue what is run, and hitting the tab >> key or CRTl-D after typing phenix.refine might auytocomplete or give a >> list of possibilities. >> >> Let me know what happened. >> >> >> Peter >> >> >> >> >> >> >> >> >> >> Ulrich Baumann wrote: >>> Hi Peter, >>> >>> I hate to bother you guys with this but .... >>> >>> dcb-macbeth:[lip3] > phenix.python >>> /usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py >>> data.file=lip_r3_1.8A.mtz model.file=in.pdb action=reindex >> standard_laws=niggli >>> #phil __OFF__ >>> ================= >>> REINDEX >>> A reindexing tool >>> ================= >>> >>> Traceback (most recent call last): >>> File >> "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py", >>> line 468, in ? >>> reindex_utils(sys.argv[1:]) >>> File >> "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py", >>> line 260, in reindex_utils >>> combined_xs = crystal.select_crystal_symmetry( >>> AttributeError: 'module' object has no attribute 'select_crystal_symmetry' >>> >>> >>> I seem to hae to set a spacegroup? Sorry, I could not find a documentation >> for >>> the reindex utility. >>> >>> Many thanks, >>> >>> Ulrich >>> >>> Quoting Peter Zwart <PHZwart(a)lbl.gov>: >>> >>>> Hi Ulrich, >>>> >>>> You could try refining your structure in a primitive setting, this might >>>> alleviate memory usage a bit (not sure though). >>>> >>>> try >>>> >>>> phenix.python $MMTBX_DIST/mmtbx/examples/reindex.py data.file=mydata.mtz >>>> model.file=mymodel.pdb action=reindex standard_laws=niggli >>>> >>>> You will get a new mtz file and a new pdb file. Unfortunately, the free >>>> flags are not copied over, so you would have to reindex those separately >>>> using iotbx.reflection_file_converter and read that file in separately >>>> in phenix.refine. >>>> >>>> This might be a bit criptic, if so, let me know and I will post more >>>> details. >>>> >>>> I am not sure this does the trick though, I hope Ralf or Pavel can give >>>> some suggestions. >>>> >>>> Cheers >>>> >>>> Peter >>>> >>>> >>>> >>>> >>>> Ulrich Baumann wrote: >>>>> Hi there, >>>>> >>>>> if you remove the ANISOU card from the input pdb file, phenix will run >>>> fine >>>>> ....sometimes not. >>>>> >>>>> phenix.refine ( Version: 2007_01_24_2154) crashed for me as well: we >> have >>>> a >>>>> rather large unit cell and good resolution. The program crashes >>>> reproducibly >>>>> (see below) when using resolution limits better than 3 A, although >>>> sometimes >>>>> this only occurs in the 2nd macrocycle. >>>>> >>>>> Working crystal symmetry after inspecting all inputs: >>>>> Unit cell: (202.401, 202.401, 317.731, 90, 90, 120) >>>>> Space group: R 3 :H (No. 146) >>>>> >>>>> >>>>> We have 2 GB memory and could stuff in more but maybe we can limit the >>>> memeory >>>>> use in a different way? >>>>> >>>>> >>>>> Thanks a lot for your help, >>>>> >>>>> Ulrich >>>>> >>>>> >>>>> ============================= ml refinement start >>>> ============================= >>>>> ----------structure factors based statistics (before >>>> refinement)---------- >>>>> Traceback (most recent call last): >>>>> File >>>> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.p >>>>> y", line 5, in <module> >>>>> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) >>>>> File >>>> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/command_li >>>>> ne.py", line 75, in run >>>>> call_back_after_monitor_collect=call_back_after_monitor_collect) >>>>> File >>>> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/driver.py" >>>>> , line 1108, in run >>>>> log = log) >>>>> File >>>> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/strategies >>>>> .py", line 174, in refinement_machine >>>>> abcd = abcd) >>>>> File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", >> line >>>> 185, >>>>> in __init__ >>>>> b_cart = b_cart) >>>>> File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", >> line >>>> 466, >>>>> in update_xray_structure >>>>> f_mask = bulk_solvent_mask_obj.structure_factors(miller_set= >>>> self.f_obs) >>>>> File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/masks.py", line >>>> 97, in >>>>> structure_factors >>>>> flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real())) >>>>> MemoryError >>>>> >>>>> ---------------------------------------------------------- >>>>> ------------------------------------------------------- >>>>> Quoting Pavel Afonine <pafonine(a)lbl.gov>: >>>>> >>>>>> Hi, >>>>>> >>>>>> this is known problem and it will be fixed ASAP; sorry for this. >>>>>> This presumably happens because an atom selected to be refined as >>>>>> individual anisotropic is included into a TLS group. >>>>>> I will let you know once the fixed version of CCI Apps is available. >>>>>> >>>>>> Pavel. >>>>>> >>>>>> >>>>>> >>>>>> Jianghai Zhu wrote: >>>>>>> Hi, >>>>>>> >>>>>>> I was using phenix.refine from the latest cci apps bundle to do >>>>>>> tls+individual_sites+individual_adp refinement. The program crashed >>>>>>> with the following error message. >>>>>>> >>>>>>> ----------Target weights (before refinement)---------- >>>>>>> >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> File >>>>>>> "/nfs/home/jzhu/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 >>>>>>> >> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/command_line.py", >>>>>>> line 75, in run >>>>>>> call_back_after_monitor_collect=call_back_after_monitor_collect) >>>>>>> File >>>>>>> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py", >>>>>>> line 1108, in run >>>>>>> log = log) >>>>>>> File >>>>>>> >> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py", >>>>>>> line 245, in refinement_machine >>>>>>> log = log) >>>>>>> File >>>>>>> >> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py", >>>>>>> line 222, in __init__ >>>>>>> compute_gradients = True) >>>>>>> File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/restraints.py", >>>>>>> line 144, in energies_adp_aniso >>>>>>> xray_structure = xray_structure, >>>>>>> File >>>>>>> >> "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", >>>>>>> line 109, in __init__ >>>>>>> self.check_flags(fl_i) >>>>>>> File >>>>>>> >> "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", >>>>>>> line 177, in check_flags >>>>>>> assert not fl.use_u_aniso() >>>>>>> AssertionError >>>>>>> >>>>>>> Anyone has any idea what is happening? Thanks. >>>>>>> >>>>>>> Jianghai >>>>>>> >>>>>>> +++++++++++++++++++++++++++++++ >>>>>>> Jianghai Zhu, Ph.D >>>>>>> CBR Institute for Biomedical Research >>>>>>> Department of Pathology >>>>>>> Harvard Medical School >>>>>>> 200 Longwood Ave., Boston, MA 02115 >>>>>>> Ph: 617-278-3211 >>>>>>> Fx: 618-278-3232 >>>>>>> +++++++++++++++++++++++++++++++ >>>>>>> >>>>>>> >>>>>>> >>>>>>> >> ------------------------------------------------------------------------ >>>>>>> _______________________________________________ >>>>>>> phenixbb mailing list >>>>>>> phenixbb(a)phenix-online.org >>>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>>>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>> >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > >

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Re: [phenixbb] pdb waters
by Pavel Afonine 16 Mar '07

16 Mar '07

Hi, yes, the waters in your file do not match the Monomer Library definition. If you simply replace O1 with O that will fix the problem. For example: GOOD record: ATOM 22792 O HOH X 1 37.309 34.504 -14.174 1.00 38.28 O BAD record: ATOM 22792 O1 HOH X 1 37.309 34.504 -14.174 1.00 38.28 O > I have tried running elbow on my pdb already with no luck. using your > command I get the error message: elbow.builder: error: no such option: > --do-all That makes me thinking that you are using an old version of CCI Apps or PHENIX. Are you using the latest one? Is the command you run looks like: % elbow.builder x.pdb --do-all Nigel: do you have any comments? Pavel.

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