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Re: [phenixbb] Problem with BOOST_ADAPTBX_FPE_DEFAULT and BOOST_ADAPTBX_SIGNALS_DEFAULT
by Sam Stampfer 25 Aug '09

25 Aug '09

Thanks for everyone's help! I got the refinement working in version 1.4-125 and am all set. -Sam On Tue, Aug 25, 2009 at 4:19 PM, Ben Eisenbraun <bene(a)crystal.harvard.edu>wrote: > There's version 1.4-125 in the SBGrid software tree. Did you try it? Is > that version too old? > > You should ask Katya to update her user list. You're not in our database. > > -ben > > On Tue, Aug 25, 2009 at 04:13:44PM -0400, Sam Stampfer wrote: > > I couldn't get the source code to compile- the final message was: "error: > > configuration step incomplete, exiting". Any ideas? > > Thanks, > > -Sam > > > > [A copy of my problem is pasted here]: > > > > I'm running the latest complete version of phenix (version 1.4-147, on > Linux > > 2.6-x86 64). When I run my .csh file I get the following error (with the > 4 > > previous lines included): > > > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd) > > [0x446bdd] > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python > > [0x4396e4] > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python > > [0x4470a9] > > /lib64/libc.so.6 [0x30fca322a0] > > 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. > > > > When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run > my > > .csh file, it runs for a slightly longer period of time before ending > with a > > different error: > > > > 311240e000-3112410000 rw-p 0000e000 fd:00 14237822 > > /lib64/libbz2.so.1.0.4 > > 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0 > > 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0 > > 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0 > > 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0 > > 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so > > 2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941 > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort > > > > However, the file ran fine and successfully output an improved .pdb file > > without any BOOST-related problems on my PI's Mac- she is running version > 95 > > of Phenix (which I was unable to obtain for linux- is it available > > somewhere?) > > > > Can you help me with this? > > > > Thanks! > > > > -Sam > > > > > > On Tue, Aug 25, 2009 at 3:28 PM, Ralf W. Grosse-Kunstleve > > <rwgk(a)cci.lbl.gov>wrote: > > > > > Could you try with a source installation? > > > > > > > > > > https://www.phenix-online.org/download/phenix/nightly/?version=1.4-147&show… > > > > > > I recommend you rm -rf the binary installation before ./install from > > > sources. > > > Add > > > --nproc=N > > > to the ./install command to use all N cpus in your machine for the > > > installation. > > > > > > Let me know if the problem persists. > > > > > > Ralf > > > _______________________________________________ > > > 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 > > > > -- > | Ben Eisenbraun | Tools Sysadmin | > | Structural Biology Grid | http://sbgrid.org | > | Harvard Medical School | http://hms.harvard.edu | > >

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Problem with BOOST_ADAPTBX_FPE_DEFAULT and BOOST_ADAPTBX_SIGNALS_DEFAULT
by Sam Stampfer 25 Aug '09

25 Aug '09

Hi, I'm running the latest complete version of phenix (version 1.4-147, on Linux 2.6-x86 64). When I run my .csh file I get the following error (with the 4 previous lines included): /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd) [0x446bdd] /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python [0x4396e4] /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python [0x4470a9] /lib64/libc.so.6 [0x30fca322a0] 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. When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run my .csh file, it runs for a slightly longer period of time before ending with a different error: 311240e000-3112410000 rw-p 0000e000 fd:00 14237822 /lib64/libbz2.so.1.0.4 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so 2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort However, the file ran fine and successfully output an improved .pdb file without any BOOST-related problems on my PI's Mac- she is running version 95 of Phenix (which I was unable to obtain for linux- is it available somewhere?) Can you help me with this? Thanks! -Sam

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ruthenium parameters
by Terry Lang 24 Aug '09

24 Aug '09

Hey Everyone, I am working on an xray structure that contains a ruthenium. I have been able to use elbow to create a cif file that phenix can read and refine without throwing error messages. However, there is a large amount of positive electron density after the refinement. I am looking into modeling coordinate waters, but I first wanted to check that the ruthenium is being read correctly by phenix. How do I figure out if it is properly recognized (eg correct scattering factors, bond and angle restraints, etc)? Thanks, Terry -- P. Therese Lang Postdoctoral Scholar Alber Lab, UC Berkeley

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phenix.refine 1.3 vs. 1.4 map quality ?
by William G. Scott 23 Aug '09

23 Aug '09

Hi folks: About a year ago I refined a 1.6 Å RNA structure with phenix.refine 1.3b-rc6 and then got distracted. I picked it up today and essentially repeated the last round of refinement with 1.4-57 (and also 1.4-159). The maps are subtly different, but consistently slightly worse with 1.4. Here are two examples: http://sage.ucsc.edu/~wgscott/mystuff/old_vs_new.pdf In the second example, this would lead to deletion of one of the octahedrally coordinated waters on a known Mg++ ion. 2OEU is similar, except 2.0 Å resolution, and it has Mn2+ instead of Mg ++. A similar thing happens with the corresponding water in that structure. Has the weighting for the bulk solvent mask or something like that been increased? Thanks. Bill Scott

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difference in B factor for NCS groups
by James Whittle 21 Aug '09

21 Aug '09

Dear all, I'm working with a structure were one NCS copy has significantly high B-factors than the other. That one copy makes few crystal contacts to stabilize it. Is there a recommended way to adjust the refinement to reflect this ... using TLS? Decreasing b_factor_weight? Is there a way refine a group_b to be added to the b-factor of each atom in that chain? --James

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Error in running Autosol....
by S. Karthikeyan 19 Aug '09

19 Aug '09

Dear All, I am using phenix-1.4-138 in RHEL5 Xeon-64 bit workstation. I am trying to solve a structure of Se-Met through phenix.autosol_gui. Once the programs starts it goes to several stages including converting from mtz to sca, xtriage and so on. Finally it gives an error message as follows: ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked See overall log file and also solve log file (in AutoSol_run_2_/LAST.LOG) ******************************************************************************** I found the LAST.LOG file is empty. I am trying to find out what could be problem? Any suggestions or help is much appreciated! Thanking you S.Karthikeyan

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Problem with LLP ligand
by James Naismith 19 Aug '09

19 Aug '09

Dear All, I am trying to refine a structure which has a Lys linked to PLP. In the PDB this is called LLP. When I take it through refine it crashes complaining about the ligand. "Sorry : Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 8 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands. Traceback: None " I know I have to use REEL to fix this in some way. I have used REEL to make ligands not bound to protein before. It is how to do this when the ligand is covalently bound that I am stuck with. Any help (particularly a cif restraints file!) gratefully received. best Jim ------------------------------------------------------------------------------- Major third-party components of Phenix include: Python, wxwidgets, wxPython, Boost, SCons, Clipper, CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------- Processing inputs. This may take a minute or two. Working crystal symmetry after inspecting all inputs: Unit cell: (50.677, 137.283, 62.258, 90, 109.637, 90) Space group: P 1 21 1 (No. 4) Monomer Library directory: "/usr/local/phenix-1.4-115/chem_data/mon_lib" Total number of atoms: 13558 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6752 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 420, 6747 Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3': 1, 'LLP,HE3': 1} Classifications: {'peptide': 420} Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4} Chain breaks: 3 Conformer: "A" Number of residues, atoms: 420, 6747 Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3': 1, 'LLP,HE3': 1} Classifications: {'peptide': 420} Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4} Chain breaks: 3 bond proxies already assigned to first conformer: 6820 Chain: "B" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6800 Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3': 1, 'LLP,HE3': 1} Classifications: {'peptide': 423} Link IDs: {'PTRANS': 14, 'TRANS': 404, 'PCIS': 4} Chain breaks: 3 Chain: "M" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' SM': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Number of atoms with unknown nonbonded energy type symbols: 8 "ATOM 3149 HG3 LLP A 211 .*. H " "ATOM 3151 HE3 LLP A 211 .*. H " "ATOM 3153 HD3 LLP A 211 .*. H " "ATOM 3155 HB3 LLP A 211 .*. H " "ATOM 9896 HG3 LLP B 211 .*. H " "ATOM 9898 HE3 LLP B 211 .*. H " "ATOM 9900 HD3 LLP B 211 .*. H " "ATOM 9902 HB3 LLP B 211 .*. H " Time building chain proxies: 9.24, per 1000 atoms: 0.68 The University of St Andrews is a charity registered in Scotland : No SC013532

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RESOLVE with RNA/protein structure at low resolution
by Peter Grey 19 Aug '09

19 Aug '09

Hello all, I try to solve the structure of RNA and RNA/protein complex at low resolution (5A). Phases come from partial model MR solution. I would really welcome advice about density modification in such cases with RESOLVE.. Does the RESOLVE database of density distributions contain RNA/protein examples ? Can RESOLVE work at low resolution given that histograms profiles are at resolutions from 1.2 A to 4 A ? Many thanks for you help, Peter.

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AutoBuild help
by Timothy C. Umland 18 Aug '09

18 Aug '09

I am new to running the AutoMR and AutoBuild Wizards, and I am having a problem getting AutoBuild to run. I have run AutoMR and it appeared to run fine, yielding a solution. However, when it did the default hand-off of the MR solution to AutoBuild, AutoBuild crashed. I then tried to run AutoBuild by itself, using the MR solution as the input model. Again, AutoBuild crashed. The error was the same in both cases. I was running AutoMR and AutoBuild from the command line. I am running Phenix version 1.4-3 on an Intel Mac (OS X 10.5.8). The AutoBuild error was **************************************************************************** **** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /AutoBuild_run_3_/TEMP0/RUN_FILE_1' sort: invalid option -- 4 Try `sort --help' for more information. **************************************************************************** **** I tried the suggested "sort --help", but at least to me it wasn't helpful. I am guessing that I have some incompatibility with my local installation of "sort" and Phenix? Any help is appreciated. Thanks, Tim

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1-2 October: What is a Macromolecular Complex ? meeting at the NKI, Amsterdam
by Anastassis Perrakis 18 Aug '09

18 Aug '09

Dear all, This is a reminder and some news for the meeting: "What is a macromolecular Complex? Shades of Meaning Across Cellular, Systems, and Structural Biology" http://xtal.nki.nl/Oct2009 - Registration closes on Monday 7th September at 12:00 noon. No exceptions after the deadline. - There will be eight (8) fellowships for attending the meeting, 500 Euro (max) each (*) Best regards on behalf of the organizers, Tassos (*) Only available if your lab is NOT part of the EU programs that support the meeting (SPINE-2-Complexes, TEACH-SG, 3D-Repertoire) and you really wanted to attend but could not for financial reasons, but 500 Euro will make it possible for you to join us, please email a.perrakis.AT.nki.nl with a short motivation and research interests, 10-15 lines max (no attachments please, simple text). Preference will be given to people not yet registered, since we might well assume that people that already registered had the money already sorted. The amount is the MAXimum available per person for ALL expenses, and it will be reimbursed after the meeting, *** based on receipts ***!

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