- phenixbb - phenix-online.org

AUTOBUILD CC
by Noinaj 06 Jul '06

06 Jul '06

Hi, I am new to PHENIX and would like to get a bit of guidance. I am helping a friend with her structure using SAD phasing. She has 4 Se/molecule with 4 mol/ASU. We used Solve to find her sites with nice occupancy, and then ran AUTOBUILD, just to see how it did. It is returning map correlation coeff, Z-scores, etc. What are good numbers for these parameters? Thanks in advance. Cheers, Nick

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Re: [phenixbb] problem when installing phenix 1.24.1b
by Petrus H Zwart 06 Jul '06

06 Jul '06

This most likely means you have downloaded the binairies that do not match your machine architecture. See the readme file: ------------------------------------------------------------------------ ----------- Currently, the following Redhat Linux platforms are tested, and therefore supported for the distribution: - Redhat 8.0 - Redhat 9.0 - Redhat Enterprise Workstation 3 [+/- x86_64] - Redhat Enterprise Server 4.2 [+/- x86_64] - Fedora Core 3 [+/- x86_64] - Fedora Core 5 [+/- x86_64] Redhat versions prior to 8.0 are not supported. PHENIX should also install on other Linux platforms such as Mandrake, or SuSe. There are 4 different Linux installations available, based on the version of the kernel (2.4 or 2.6) and the CPU type (ix86 or x86_64). If it isn't clear which you need then type this command on the machine in question: % uname -rm The first item is the kernel version, the second is the machine hardware. Please download the appropriate installer based on this table: ------------------------------------------------------------------------ - | hardware \ kernel | 2.4 | 2.6 | ------------------------------------------------------------------------ - | ix86 | intel-linux-2.4 | intel-linux-2.6 | ------------------------------------------------------------------------ - | x86_64 | intel-linux-2.4-x86_64| intel-linux-2.6- x86_64| ------------------------------------------------------------------------ - Currently, the following other Unix platforms are tested, and therefore supported for the distribution: - Compaq Tru64 5.1 - SGI Irix 6.5[*] ------------------------------------------------------------------------ ------------ i.e., check if if you have a 2.4 or 2.6 linux kernel and what your cpu type is. for me, I get this: 2.6.11-1.1369_FC4smp i686 i.e, i need the 2.6 , ix86 version. HTH Peter Hi, I met a problem when installing the phenix 1.24.1a. The installer gave me an error information "neither source nor binary availabe, exiting installation". What's wrong with my installation? Zhongli _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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problem when installing phenix 1.24.1b
by 崔中利 06 Jul '06

06 Jul '06

Hi, I met a problem when installing the phenix 1.24.1a. The installer gave me an error information "neither source nor binary availabe, exiting installation". What's wrong with my installation? Zhongli

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run phenix in vitue linux environment
by 崔中利 06 Jul '06

06 Jul '06

I installed phenix 1.1a in a virtue Fedora Core 3 machine with VMware workstation 5 under windows XP on a IBM X31 notebook. When I run autosol (sad) to solve my protein, the system gave me error information "the connection to strategy disrupted" after all parameters are set, but it seems that the program is still running (for the window is still green) . However, the Autosol is showed as Finished in Job control window. Even if I leave the program running overnight, there is no solution produced. Can anyome give me some comments? Zhongli

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PHENIX 1.24.1 beta now available
by Paul Adams 06 Jul '06

06 Jul '06

======================================================================= PHENIX 1.24.1 Beta Release ======================================================================= On behalf of the PHENIX development team I am happy to announce that the next general release version of PHENIX is now available. Binary installers for Linux, SGI and Tru64 platforms are available at our download site: http://phenix-online.org/download/ Current users of PHENIX should upgrade to this most recent release version. To obtain download instructions visit: http://phenix-online.org/phenix_request/ Documentation for PHENIX is available at: http://phenix-online.org/download/documentation/phenix/ There is a PHENIX mailing list at: http://www.phenix-online.org/mailman/listinfo/phenixbb/ There is a PHENIX wiki at: http://www.phenix-online.org/phenix_wiki Please consult the installer README file or online documentation for installation instructions. This is a beta test version, and we therefore look forward to feedback and bug reports from users. Please direct questions and problem reports to: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to PHENIX should visit the PHENIX website for information about the PHENIX Industrial Consortium: http://www.phenix-online.org/ This version of PHENIX has three main user interfaces: command-line tools, strategies and wizards. Wizards are available under the Wizard tab in the PHENIX GUI, and are designed to complete a complex structure determination process, making automatic decisions when possible, but prompting the user for additional information when necessary. Strategies are available under the Strategy tab in the PHENIX GUI, and are networks of tasks constructed to perform higher-level functions. Version 1.24.1b of PHENIX includes: Wizards (in the PHENIX GUI and from the command-line) ===================================================== - AutoSol - automated structure solution (from processed data to a first map and model) using HySS, SOLVE, RESOLVE, and phenix.refine. - AutoMR - automated molecular replacement, using PHASER. Followed by automated model rebuilding using the AutoBuild wizard. - AutoBuild - automated model building or rebuilding combined with structure refinement, using RESOLVE and phenix.refine. - AutoLig - automated ligand fitting into difference density maps using RESOLVE once a complete protein model is available. Strategies (in the PHENIX GUI) ============================== - Ligand screening against the top 200 ligands in the PDB, using RESOLVE. - Structure solution (MAD/SAD and SIR(AS)/MIR(AS)) combining HySS, SOLVE and RESOLVE. - Phase improvement using maximum likelihood methods in RESOLVE. - Model building using TEXTAL or RESOLVE. Command-line tools ================== - mmtbx.xtriage (comprehensive data quality assessment, including twin analysis) - iotbx.reflection_statistics (analysis of diffraction data) - mmtbx.fest (FA value calculation) - phenix.hyss (anomalous substructure determination) - textal.build (automated model building with TEXTAL) - elbow.builder (generation of ligand coordinates and restraints) - phenix.refine (automated structure refinement) - phenix.geometry_minimization (regularize a structure) - phenix.solve (solve) - phenix.resolve (resolve) - phenix.resolve_pattern (resolve_pattern) - iotbx.mtz.dump (write useful information about a MTZ file) - iotbx.pdb.hierarchy (write useful information about a PDB file) Citing PHENIX ============= If you use PHENIX for solving a structure please cite this publication: PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002). PHENIX Developers ================= Lawrence Berkeley National Laboratory - Paul D. Adams - Pavel Afonine - Ralf W. Grosse-Kunstleve - Nigel W. Moriarty - Nicholas K. Sauter - Peter H. Zwart Los Alamos National Laboratory - Tom C. Terwilliger - Li-Wei Hung - Thiru Radhakannan University of Cambridge - Randy J. Read - Airlie J. McCoy - Laurent C. Storoni Texas A&M University - Jim C. Sacchettini - Tom R. Ioerger - Kresha Gopal - Lalji Kanbi - Erik McKee - Reetal K. Pai - Tod D. Romo - Jacob N. Smith Acknowledgements ================ We are very grateful to the following for making code or libraries available to us: - Alexei Vagin and Garib Murshudov for the CCP4 Monomer Library. - The CCP4 developers for making the MTZ library available to us. - Kevin Cowtan for contributing to the cctbx reciprocal space asymmetric units. - David Abrahams for developing the Boost.Python library. Funding ======= The development of PHENIX is principally funded through the Protein Structure Initiative of the National Institute of General Medical Sciences (NIH) under grant P01GM063210. For further information about the Protein Structure Initiative please visit: http://www.nigms.nih.gov/psi/ We also acknowledge the generous support of the members of the PHENIX Industrial Consortium. For more details please visit: http://www.phenix-online.org/ ======================================================================= PHENIX 1.24.1 Beta Release ======================================================================= -- ========================================================== | Paul Adams, | | Senior Staff Scientist, Physical Biosciences Division | | Head, Berkeley Center for Structural Biology | | Deputy PI, Berkeley Structural Genomics Center | |--------------------------------------------------------| | Building 64, Room 248 | Lawrence Berkeley Laboratory, | | Tel: 510-486-4225 | 1 Cyclotron Road, | | FAX: 510-486-5909 | BLDG 64R0121, | | mailto:[email protected] | Berkeley, CA 94720, USA. | ==========================================================

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New version of Phenix
by 崔中利 05 Jul '06

05 Jul '06

Dear administrator, I have seen the introduction to 1.24.1 beta version of phenix. Why is it still not avalable for download? What is the improvement comparing to version 1.1 alpha? Zhongli

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Problem with remotely displaying PHENIX
by Luca Jovine 01 Jun '06

01 Jun '06

Dear all, While waiting for a Mac OS X version of PHENIX, I have installed it on a Linux server, with the idea of remotely display the GUI on our OS X machines. However, when I try to do so, the GUI briefly opens and then bombs out with the following message: LINUX> phenix Running the PHENIX GUI with /home/xray/luca/bin/phenix/phenix-1.1a/phenix-1.1a/ build/intel-linux/python/bin/python PHENIX distribution located in /home/xray/luca/bin/phenix/ phenix-1.1a/phenix-1.1a/phenix Variable SSH_PATH set to /usr/bin/ssh Variable PYMOL_PATH set to /home/xray/luca/bin/phenix/ phenix-1.1a/phenix-1.1a/pymol Variable RSH_PATH set to /usr/bin/rsh Project Details Project Name: luca Date Stamp : Thu Jun 01 15:56:23 2006 Machine : localhost Directory : /home/xray/luca PDS Server will be on ---------- localhost (localhost) ---------- /home/xray/luca ---------- Port 28537 PID 25355 PDS Server Details User : luca Machine : localhost Directory : /home/xray/luca Port : 28537 PID : 25374 Creating new Data Storage /home/xray/luca/strategies The program 'wxPhenix.py' received an X Window System error. This probably reflects a bug in the program. The error was 'BadWindow (invalid Window parameter)'. (Details: serial 6349 error_code 3 request_code 38 minor_code 0) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) ...has anyone else encountered the same issue, and, if so, managed to solve it? Thanks in advance and best regards, Luca ----------------------------------------------------- Luca Jovine, Ph.D. Karolinska Institutet Department of Biosciences and Nutrition Center for Structural Biochemistry (CSB) Hälsovägen 7, S-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290 E-mail: luca.jovine(a)biosci.ki.se W3: http://www.biosci.ki.se/groups/ljo/ -----------------------------------------------------

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HKL2000 and Phenix?
by ckielkop 23 May '06

23 May '06

Hi, I wonder if anyone else has had trouble running both Phenix and HKL2000 on the same linux workstation? Once Phenix we have installed and used Phenix, the HKL2000 cr_info license becomes invalid, and vice versa. A linux guru suggested in passing that our bash system has a 'license' file that gives the directories of the licenses somewhere, and that this file needs both license directories added explicitly. But where would this file be? Thanks for the help! Clara

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TEXTAL Model from map
by Andrzej LYSKOWSKI 09 May '06

09 May '06

Hi, I have one question and one problem. TEXTAL expects map in X-PLOR format but what kind of map? One can make a number of different maps in CCP4 (simple, mFo-nFc, etc.). Which type make TEXTAL happy? I've tried to run 'Build Complete Model from map' strategy and what ever I do it seems to get stuck at: Stitching and Filtering C-alpha chains... - simply nothing happens anymore. What could be a problem? Just to mention it does build a model when I use '... from mtz' strategy. MfG, Andrzej -- < Andrzej Lyskowski (andrzej[dot]lyskowski[at]uni-graz[dot]at) < Chemistry Institute - Phys. Chem./Structural Biology < Heinrichstrasse 28 < A-8010 Graz, Austria < Tel.: 43 316 380 54 69 < Fax.: 34 316 380 98 50 > A designer knows he has achieved perfection > not when there is nothing left to add, > but when there is nothing left to take away. > Antoine de Saint-Exupery

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Judging AutoSol Output
by agb838＠mail.usask.ca 30 Apr '06

30 Apr '06

I have some basic questions about the output from Phenix. Basically I have a data set that gave a solution, but I am not exactly sure how to tell about the quality of the solution from the outputs. The overall score is 110. I am not sure exactly what that refers to or how good/bad it is. I have attached the AutoSol.output file. Any basic suggestions at what I should be looking at, or if this is even the right file, would be helpful. The resolve.mtz and resolve.pdb look alright. They are a good start, but much improvement is needed. If anyone has some suggestions as to how to improve the output, that would also be helpful. I have also run the data through solve/resolve through the command prompt and it repeatedly locates four heavy atom sites (the data set is SAD). Yet, when Phenix is used, 16 sites are found. Why the difference and how do I tell what is working better and why. Thank you, Angela Hoffort

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Re: [phenixbb] Judging AutoSol Output
by Petrus H Zwart 30 Apr '06

30 Apr '06

----- Original Message ----- From: agb838(a)mail.usask.ca Date: Monday, April 24, 2006 3:18 pm Subject: [phenixbb] Judging AutoSol Output > I have some basic questions about the output from Phenix. > Basically I > have a data set that gave a solution, but I am not exactly sure > how to > tell about the quality of the solution from the outputs. The overall > score is 110. I am not sure exactly what that refers to or how > good/badit is. I have attached the AutoSol.output file. Any basic > suggestions at > what I should be looking at, or if this is even the right file, > would be > helpful. The resolve.mtz and resolve.pdb look alright. They are a good > start, but much improvement is needed. If anyone has some > suggestions as > to how to improve the output, that would also be helpful. > > I have also run the data through solve/resolve through the command > prompt and it repeatedly locates four heavy atom sites (the data > set is > SAD). Yet, when Phenix is used, 16 sites are found. Why the difference > and how do I tell what is working better and why. > Autosol is finding sites using HySS and subsequently iterates phasing, solvent flattening with the use of difference maps to find more sites. Juding from your output, it find most sites in 1 go. If you want to compare sites you find by Solve, Hyss, or famous programs from Buffalo or Goettingen, use iotbx.emma ha_from_autosol.pdb other.pdb To get an idea how many sites are matching. As far as I understand it, the overall score is a score relative to the other hand and other solutions and its absolute value is not so important, as long as it is (much) larger that any other solution. In your case, solution 1 has a score of 110, solution has a solution of 63. It is also finding NCS, which seems to be good (NCS correlation of 0.66 early no allready). Improvement of the pdb file is obtained by runnnig the modelbuild wizard I think. The Autosol wizard only carries out a limit number of model building cycles and the modelbuild wizard does a more thorough job. HTH Peter _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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phenix.refine Crashes with "ZeroDivisionError: float division"
by Dale Tronrud 14 Apr '06

14 Apr '06

Hi, I'm new to phenix and phenix.refine. I am trying to refine a protein with phenix.refine but the program crashes quite quickly. I have appended all of the output below, but the critical part is (I believe): File "/usr/local/phenix-1.1a/cctbx/cctbx/miller.py", line 432, in auto_anomalous anomalous_flag = (2*self.n_bijvoet_pairs()/self.indices().size() ZeroDivisionError: float division Apparently, self.indices().size() is zero, but I don't know why or really what that is. My mtz file does not contain any anomalous data. It just has F, SigF, and a free R flag for the positive octant of data. (Well, since this is P6122 the positive duodecant.) Any advise would be appreciated. Dale Tronrud # Date 2006-04-14 Time 15:14:52 PDT -0700 #phil __OFF__ ------------------------------------------------------------------------------ PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.1a Platform: intel-linux linux User: dale ------------------------------------------------------------------------------ phenix.refine: Macromolecular Structure Refinement ------------------------------------------------------------------------------ Phenix developers include: P.D. Adams, P. Afonine, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.K. Pai, R.J. Read, T.D. Romo, J.C. Sacchettini, N.K. Sauter, L.C. Storoni, T.C. Terwilliger Phenix home page: http://www.phenix-online.org/ ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Phenix components are copyrighted by: - Lawrence Berkeley National Laboratory - Los Alamos National Laboratory - University of Cambridge - Texas Agricultural Experiment Station & Texas Engineering Experiment Station ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Major third-party components of Phenix include: Python, wxPython, Boost, SCons, Clipper, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------ Processing inputs. This may take a minute or two. Crystal symmetry: Unit cell: (93.016, 93.016, 130.096, 90, 90, 120) Space group: P 61 2 2 (No. 178) phs1rb-coot-1-no-peak.pdb Total number of atoms: 2733 Number of models: 1 Model: 0 Number of conformers: 3 Conformer: "A" Number of atoms: 2723 Number of chains: 5 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} Number of residues, atoms: 315, 2389 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Number of residues, atoms: 6, 11 Unusual residues: {' ZN': 1, ' CA': 4} Inner-chain residues flagged as termini: ['ALA, ,316, , '] Classifications: {'unknown': 5, 'peptide': 1} Modifications used: {'COO': 1} Link IDs: {None: 5} Number of residues, atoms: 299, 299 Classifications: {'water': 299} Link IDs: {None: 298} Conformer: "B" Number of atoms: 2723 Common with "A": 2718 Number of chains: 5 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 315, 2389 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 2442 Number of residues, atoms: 6, 11 Unusual residues: {' ZN': 1, ' CA': 4} Inner-chain residues flagged as termini: ['ALA, ,316, , '] Classifications: {'unknown': 5, 'peptide': 1} Modifications used: {'COO': 1} Link IDs: {None: 5} bond proxies already assigned to first conformer: 5 Number of residues, atoms: 299, 299 Classifications: {'water': 299} Link IDs: {None: 298} Conformer: "C" Number of atoms: 2723 Common with "A": 2718 Common with "B": 2718 Number of chains: 5 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 315, 2389 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 2442 Number of residues, atoms: 6, 11 Unusual residues: {' ZN': 1, ' CA': 4} Inner-chain residues flagged as termini: ['ALA, ,316, , '] Classifications: {'unknown': 5, 'peptide': 1} Modifications used: {'COO': 1} Link IDs: {None: 5} bond proxies already assigned to first conformer: 5 Number of residues, atoms: 299, 299 Classifications: {'water': 299} Link IDs: {None: 298} Time building chain proxies: 12.22, per 1000 atoms: 4.47 Traceback (most recent call last): File "/usr/local/phenix-1.1a/phenix/phenix/command_line/refine.py", line 5, in ? command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 35, in run log=log) File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 128, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 337, in reflection_file_server err=self.log) File "/usr/local/phenix-1.1a/iotbx/iotbx/reflection_file_utils.py", line 303, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.1a/iotbx/iotbx/reflection_file_reader.py", line 160, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 363, in as_miller_arrays dataset=dataset) File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 495, in group_columns observation_type=observation_type)) File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 516, in column_group indices=group.indices).auto_anomalous(min_fraction_bijvoet_pairs=2/3.) File "/usr/local/phenix-1.1a/cctbx/cctbx/miller.py", line 432, in auto_anomalous anomalous_flag = (2*self.n_bijvoet_pairs()/self.indices().size() ZeroDivisionError: float division

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Passing keyword to a Wizard
by Andrzej LYSKOWSKI 24 Mar '06

24 Mar '06

Hi, I'm getting a feedback from AutoBuild Wizard that I should set it with coarse_grid keyword (info from LAST.LOG). However, this keyword isn't present in Set Variable menu. How can set it? Regards, Andrzej -- < Andrzej Lyskowski (andrzej[dot]lyskowski[at]uni-graz[dot]at) < Chemistry Institute - Phys. Chem./Structural Biology < Heinrichstrasse 28 < A-8010 Graz, Austria < Tel.: 43 316 380 54 69 < Fax.: 34 316 380 98 50 > A designer knows he has achieved perfection > not when there is nothing left to add, > but when there is nothing left to take away. > Antoine de Saint-Exupery

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Re: [phenixbb] PHENIX installation issues
by Ralf W. Grosse-Kunstleve 14 Mar '06

14 Mar '06

> > Another thing is i installed in a user so whenever i do project it > gives permission denied . I suspect you have the following situation: drwx------ 2 rwgk cci 4096 Mar 14 10:47 phenix-1.1a I.e. when you installed phenix the "umask" was set such that "group" and/or "others" don't have read permission. Please verify my suspicion with ls -d $PHENIX If you see the "drwx------" or maybe "drwxr-x---" it is easy to fix. Use the su command to become root, then: find phenix-1.1a -exec chmod go+r {} \; find phenix-1.1a -type d -exec chmod go+x {} \; Cheers, Ralf

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PHENIX installation issues
by Peter Zwart 14 Mar '06

14 Mar '06

I see. Unfortunately, the switching between bash and csh is needed until the next release. I am not quite sure what this > Another thing is i installed in a user so whenever i do project it gives permission denied . error/problem exactly is or how it can be solved, but maybe some of my collegues have an idea. Peter Ethayathulla Abdulsamath wrote: > hi Petrus: > > yes, it got installed I replied in phenixbb. > > But problem is everytime i have to do csh then source phenix_env file. > Then again change back to bash. > > Another thing is i installed in a user so whenever i do project it > gives permission denied . > > Everytime i logged in root then do thinz IS there any sol for it >

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Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Ralf W. Grosse-Kunstleve 13 Mar '06

13 Mar '06

> > how to change bash setup ot csh. > > I guess you can change shell (type csh or so) in a single window for > installing, sourcing Exactly. > and running phenix. Not necessarily. This trick should work: bash prompt $ csh csh prompt % source phenix_env csh prompt % bash bash prompt $ Providing a phenix_env.sh is on our todo list. Cheers, Ralf

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Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Petrus H Zwart 13 Mar '06

13 Mar '06

> how to change bash setup ot csh. I guess you can change shell (type csh or so) in a single window for installing, sourcing and running phenix. > In ccp4 there is a file for everything but how to i do for Phenix ! Yes. It is a bit clumsy, I agree. However note that the release you have is still an alpha release (http://en.wikipedia.org/wiki/Development_stage), indicating that not everything is as much in place as one might like it to be. Let us know if you have any (additional) problems. HTH Peter _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Ethayathulla A.S 12 Mar '06

12 Mar '06

Dear peter: how to change bash setup ot csh. I understood that the program is written for csh and tcsh how do change to bash format so that it gets installed In ccp4 there is a file for everything but how to i do for Phenix ! Thanking you Ethayathulla

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Re: [phenixbb] Regarding installation
by Petrus H Zwart 10 Mar '06

10 Mar '06

Hai Ethayathulla, Have a look at the following posting: http://www.phenix-online.org/pipermail/phenixbb/2006- February/000004.html i.e., things do not work in bash, but do in csh/tcsh. HTH Peter Hi I tried to install Phenix in RED HAT 9.0 LINUX It got installed succesfully But when tried to source it gives error message bash :/ command not found :/usr/local/phenix1.1a/phenix_env line 38 unexpected end of line plz suggest Thanking you -- A.S.Ethayathulla Department of BIophysics All India Institute of Medical Sciences Ansai Nagar New Delhi-110029 India _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Regarding installation
by Ethayathulla A.S 10 Mar '06

10 Mar '06

Hi I tried to install Phenix in RED HAT 9.0 LINUX It got installed succesfully But when tried to source it gives error message bash :/ command not found :/usr/local/phenix1.1a/phenix_env line 38 unexpected end of line plz suggest Thanking you -- A.S.Ethayathulla Department of BIophysics All India Institute of Medical Sciences Ansai Nagar New Delhi-110029 India

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Re: [phenixbb] bug? iotbx.reflection_statistics apparent
by Ralf W. Grosse-Kunstleve 06 Mar '06

06 Mar '06

> I tried supplying the space group in the command line using the > --symmetry I think there is another bug there - the command line > symmetry does not override the (wrong) symmetry that the routine gets > from the .sca file I am afraid you are right again. I forgot to include the plumbing for the --force_symmetry option. Sorry, this is getting ugly. To use your unmerged reflection file, edit this Python script in the iotbx tree: echo `libtbx.show_dist_paths iotbx`/iotbx/scalepack/no_merge_original_index.py Replace all "force_symmetry=False" with "force_symmetry=True", then try again.

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Re: [phenixbb] bug? iotbx.reflection_statistics apparent space group error reading scalepack .sca file
by Ralf W. Grosse-Kunstleve 06 Mar '06

06 Mar '06

> iotbx.reflection_statistics returns space group 195 > for a scalepack 'no merge original index' .sca file for > space group 123 (i.e space group 197) > > the first line of the .sca file is > 12 i23 You are right, this is a bug. Sorry. However, it went unnoticed because we usually supply the correct space group (along with the missing unit cell parameters) via --symmetry=some_other_file You could also use --unit_cell=10,20,30,90,90,90 --space_group=197 Mostly I prefer --symmetry because there is less of a chance to mistype. Also, quite often the space group in a reflection file is not correct anyway (e.g. P222 vs. P212121). > the CCP4 program scala can output a 'no merge original index' format > file, which has all 24 i23 symmetry operators in the header - but > iotbx.reflection_statistics cannot read that either I think you should be able to use the .sca file with the --symmetry or --space_group option. I've never tried to work with scala 'no merge original index' files. If you could send me your files I will look into fixing both problems. Peter Zwart wrote: > Note that iotbx.reflection statistics itself performs a merging step, > which is less sophisticated then those available in SCALA or scalepack. > Therefor, it might be worthwile considering supplying merged data to > iotbx.reflection_statistics. That's right. The simple merging in the cctbx is meant to be a stop-gap measure. It is best to merge externally with a program specifically designed for this purpose. Thanks for reporting the bug! Cheers, Ralf

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bug? iotbx.reflection_statistics apparent space group error reading scalepack .sca file
by Peter Metcalf 06 Mar '06

06 Mar '06

Hi - I hope this is the right place to post this iotbx.reflection_statistics returns space group 195 for a scalepack 'no merge original index' .sca file for space group 123 (i.e space group 197) the first line of the .sca file is 12 i23 the CCP4 program scala can output a 'no merge original index' format file, which has all 24 i23 symmetry operators in the header - but iotbx.reflection_statistics cannot read that either cheers Peter Metcalf

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Re: [phenixbb] unknown space group problem
by Thomas C. Terwilliger 03 Mar '06

03 Mar '06

Hi Angela, Thanks for sending me the data. I'm sorry about the problem reading your mtz files. The problem with reading the files is that some of the amplitudes in the mtz files are very big, leading to overflows written out as "****" when AutoSol converts them to .sca files. This problem is fixed in the current version of AutoSol, but that doesn't help you much. In the meantime, the solution is to convert the mtz files to sca and scale them so they don't overflow. I used phenix to do this with iotbx.reflection_file_converter idhrem_i23.mtz --label='F_refm101(+)' --sca=rem.sca to do this. The 3 .sca files seem to run ok now. I'm having trouble sending attachments so I didn't attach it, but if you have trouble reproducing my result I'll be happy to send you the converted files. All the best, Tom T > > > ----- Original Message ----- > From: Tom Terwilliger <terwilliger(a)lanl.gov> > Date: Thursday, March 2, 2006 4:48 pm > Subject: Re: [phenixbb] unknown space group problem > >> Hi Angela, >> Thanks! Yes, could you please rename the zip file to ".txt" and re- >> send? >> Our email system deletes all zip files! >> Thanks! >> -Tom T >> >> >> >> 3/2/2006 -0600, you wrote: >> >I am sending the output where the label error occurs as well as a zip >> >file with the three merged mtz files. I hope a zip file is okay, >> if it >> >isn't, let me know and I can try and get a tar file. These data sets >> >have been integrated in I23. >> > >> >I have been trying to reintegrate the data in H3 as suggested, but >> >Mosflm is giving me a lot of problems with this space group. The >> >predictions don't align with the reflections and sometimes it crashes >> >(this was not a problem with R3 or I23). >> > >> >Thanks, >> >Angela >> > >> >X-PMX-Wrap: 60 >> > >> >An executable email attachment called idhpk_i23.zip >> >(content_type:application/x-zip-compressed, size:7039478 bytes) >> was >> >removed from this message by LANL network as a security precaution. >> > >> >Please see http://network.lanl.gov/email/virus-scan.shtml for >> additional >> >information. >> >> >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: >> http://solve.lanl.govTB Structural Genomics Consortium web site: >> http://www.doe-mbi.ucla.edu/TB >> >> >

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Re: [phenixbb] unknown space group problems
by Banumathi Sankaran 02 Mar '06

02 Mar '06

can u send me the drs phone number pa Tom, If this lady does indeed send you the data, Would you be so kind to run the latest version of xtriage on it to see wheter or not tyhe spacegroup is correct? Thomas C. Terwilliger wrote: >Hi Angela, > >I think the solution to the first problem is to index your data in the >space group H3 instead of R3 (the hexagonal setting of R3 rather than the >rhombohedral setting). This is the convention these days in many >programs, including in the AutoSol wizard. > >The second problem I'm a little less clear on. Can you send me some output >where this happens (or if you like, a tar file with the data) and I'll >have a look at it? >Regards, >Tom T > > > > >>I am trying to sovle MAD data using the PHENIX software. I am using the >>AutoSol >>wizard. My data is integrated in R3. Phenix keeps spitting out the error >>that >>this space group is either unknown or the cell dimensions are >>inappropriate to >>the space group (the are a=b=c=159 and alpha=beta=gamma=109). Is there a >>glitch >>with thi space group or am I doing something wrong. Phaser tends to have >>the >>same problem with this space group and I can not seem to get around it. >> >>If I provide data in a different space group I can get past this problem >>only to >>be confronted with another problem regarding the column labels in my mtz >>files. >>I have six data sets collected. Two for each of three different >>wavelengths. >>Each of the two for a single wavelength is scaled seperately and then >>merged >>together using ccp4. I have taken a lot of effort to make sure that the >>column >>labels do not repeat in these files, yet I continually get column label >>errors >>when I run three mtz files in the AutoSol wizard (one mtz file for each >>wavelength). I am getting the same errors in ccp4 as well. There must be >>something basic that I am doing wrong with regards to processing my data >>and >>merging the mtzs together. >> >>Thanks you for your help. >>Angela >> >>_______________________________________________ >>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] unknown space group problems
by Banumathi Sankaran 02 Mar '06

02 Mar '06

I am sorry i sent my previous mail by mistake Banu Tom, If this lady does indeed send you the data, Would you be so kind to run the latest version of xtriage on it to see wheter or not tyhe spacegroup is correct? Thomas C. Terwilliger wrote: >Hi Angela, > >I think the solution to the first problem is to index your data in the >space group H3 instead of R3 (the hexagonal setting of R3 rather than the >rhombohedral setting). This is the convention these days in many >programs, including in the AutoSol wizard. > >The second problem I'm a little less clear on. Can you send me some output >where this happens (or if you like, a tar file with the data) and I'll >have a look at it? >Regards, >Tom T > > > > >>I am trying to sovle MAD data using the PHENIX software. I am using the >>AutoSol >>wizard. My data is integrated in R3. Phenix keeps spitting out the error >>that >>this space group is either unknown or the cell dimensions are >>inappropriate to >>the space group (the are a=b=c=159 and alpha=beta=gamma=109). Is there a >>glitch >>with thi space group or am I doing something wrong. Phaser tends to have >>the >>same problem with this space group and I can not seem to get around it. >> >>If I provide data in a different space group I can get past this problem >>only to >>be confronted with another problem regarding the column labels in my mtz >>files. >>I have six data sets collected. Two for each of three different >>wavelengths. >>Each of the two for a single wavelength is scaled seperately and then >>merged >>together using ccp4. I have taken a lot of effort to make sure that the >>column >>labels do not repeat in these files, yet I continually get column label >>errors >>when I run three mtz files in the AutoSol wizard (one mtz file for each >>wavelength). I am getting the same errors in ccp4 as well. There must be >>something basic that I am doing wrong with regards to processing my data >>and >>merging the mtzs together. >> >>Thanks you for your help. >>Angela >> >>_______________________________________________ >>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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unknown space group problems
by Angela Hoffort 01 Mar '06

01 Mar '06

I am trying to sovle MAD data using the PHENIX software. I am using the AutoSol wizard. My data is integrated in R3. Phenix keeps spitting out the error that this space group is either unknown or the cell dimensions are inappropriate to the space group (the are a=b=c=159 and alpha=beta=gamma=109). Is there a glitch with thi space group or am I doing something wrong. Phaser tends to have the same problem with this space group and I can not seem to get around it. If I provide data in a different space group I can get past this problem only to be confronted with another problem regarding the column labels in my mtz files. I have six data sets collected. Two for each of three different wavelengths. Each of the two for a single wavelength is scaled seperately and then merged together using ccp4. I have taken a lot of effort to make sure that the column labels do not repeat in these files, yet I continually get column label errors when I run three mtz files in the AutoSol wizard (one mtz file for each wavelength). I am getting the same errors in ccp4 as well. There must be something basic that I am doing wrong with regards to processing my data and merging the mtzs together. Thanks you for your help. Angela

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installing phenix
by Kielkopf, Clara L. 10 Feb '06

10 Feb '06

I'm a linux novice installing Phenix on our linux boxes, running Fedora Core 3 in the bash shell. THe install script runs without error, and the new phenix-1.1a directory is created in /usr/local. However, I have to switch to csh before running the program. Even after setting the environmental variables correctly, the program wouldn't run in the bash shell. Is there a simple modification to run in bash? Thank you.

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Problems in installation Phenix1.1a on Linux redhat F4
by Cheng Luo, Ph.D. 07 Jan '06

07 Jan '06

Dear Phenix users, I am a new user of phenix. When I install it in a new machine installed Linux F4, I meet a problem in gtk. I paste the information( the reported err is in red words). " generating PHENIX environment setup script creating /marmor9/pub/bin/phenix-1.1a/phenix_env generating libtbx environment additions creating $PHENIX_BUILD/dispatcher_include_phenix.sh setting environment configuring PHENIX components /marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/bin/gtk-query-immodules-2.0: error while loading shared libraries: /marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/libgdk-x11-2.0.so.0: cannot restore segment prot after reloc: Permission denied generating gdk-pixbuf.loaders file" .....other is ok After installation, i source the env and run with phenix command, it told me these errors: File "/marmor9/pub/bin/phenix-1.1a/phenix/wxGUI/wxPhenix.py", line 11, in ? from wxPython.wx import * File "/marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/python2.4/site-packages/wx-2.5.3-gtk2-ansi/wxPython/__init__.py", line 10, in ? import _wx File "/marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/python2.4/site-packages/wx-2.5.3-gtk2-ansi/wxPython/_wx.py", line 3, in ? from _core import * File "/marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/python2.4/site-packages/wx-2.5.3-gtk2-ansi/wxPython/_core.py", line 15, in ? import wx._core File "/marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/python2.4/site-packages/wx-2.5.3-gtk2-ansi/wx/__init__.py", line 42, in ? from wx._core import * File "/marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/python2.4/site-packages/wx-2.5.3-gtk2-ansi/wx/_core.py", line 4, in ? import _core_ ImportError: /marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/libgdk-x11-2.0.so.0: cannot restore segment prot after reloc: Permission denied Then I share this disk and source and run in another machine install red-hat 9, it did work. So maybe some library configurations are different, but since I have no too much experience about it. Is it possible for your expert give me some suggestion? Thank you in advance for your any suggestions! Best regards, Cheng Luo, Ph.D. Cheng Luo, Ph.D. Marmorstein's Lab Room 327,3601 Spruce StreetThe Wistar Institute PA(19104) USA Tel:215-898-2304 2006-01-06

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test
by Paul Adams 14 Aug '05

14 Aug '05

-- ========================================================== | Paul Adams | | Staff Scientist, Physical Biosciences Division | | Head, Berkeley Center for Structural Biology | | Deputy PI, Berkeley Structural Genomics Center | |--------------------------------------------------------| | Building 64, Room 248 | Lawrence Berkeley Laboratory, | | Tel: 510-486-4225 | 1 Cyclotron Road, | | FAX: 510-486-5909 | BLDG 64R0121, | | mailto:[email protected] | Berkeley, CA 94720, USA. | ==========================================================

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