- phenixbb - phenix-online.org

Transfer to new computer
by Colin Levy 15 Mar '12

15 Mar '12

Hi, Is it possible to transfer Phenix along with it's archive to a new computer? I have a fresh install of Phenix on the new machine and a copy of all the original files and folders from the old machine but cant figure how to point Phenix to the correct place. Thanks Colin

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March 15, 2012 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 Mar '12

14 Mar '12

Dear Users, The deadline for May/June 2012 Collaborative Crystallography proposals will be *Mar 15, 2012. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ------------------------------------------------------------ ----------------------------- How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for May/June 2012 allocation period, proposals must be submitted by *March 15, 2012.* The deadline for CC proposals for the time period July/August 2012 will be May 15, 2012. Regards, Banumathi Sankaran

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David Sayre
by Paul Adams 12 Mar '12

12 Mar '12

On behalf of the Phenix development team: We regret deeply the passing of David Sayre on Feb. 23, 2012. David Sayre made profound contributions to crystallography and scientific computing that continue to have a major impact decades later. An obituary summarizing his many achievements was posted by Physics Today (http://www.physicstoday.org/1.2732466). In crystallography, Sayre’s fundamental insight into the implications of the atomic nature of crystal structures and the relationships between crystallographic structure factors allowed him to develop in 1952 the brilliantly simple Sayre equation relating each structure factor to all other structure factors. The Sayre equation has had a well-known yet greatly under-appreciated significance in small-molecule crystallography, both in its original form and in the equivalent probabilistic forms implemented later as part of direct methods. These methods have profoundly affected macromolecular crystallography in the last decade because of their astounding power for determination of heavy-atom substructures. The use of direct methods has made possible solution of the positions of as many as 160 selenium atoms in large macromolecular structures. To appreciate the feat that this represents, it is useful to consider that many macromolecular crystallographers were initially hesitant to use the seleno-methionine approach at all for structures that had more than about 10 selenium atoms for fear that the substructure could not be solved. Sayre’s recent work on phasing X-ray diffraction data from single large objects such as a yeast cell and single small objects such as a single protein molecule was groundbreaking in a different way. This work is revolutionary because of its boldness, and because of the elegantly simple approach to phase determination that Sayre developed. Once again Sayre took a fundamental real-space feature of the diffraction image and used it to obtain phase relationships. In this case the diffraction forms a continuous pattern from a single object, and the feature is the lack of contrast outside of the object. While the idea of using a mask of the object (the “support”) to define phases has been used for some time in many contexts, it was far from obvious that this could be done with a single cell or with a single protein molecule. Sayre and his colleagues systematically showed theoretically and then experimentally that each step in this process can be carried out and that the required signal can be extracted to obtain an X-ray image of microdots and later even a yeast cell. Others have followed up his ideas for phasing data from a single protein molecule. This work was of fundamental and transforming importance because few would have believed that the ideas were remotely feasible, and now they have a sound theoretical basis and experimental demonstrations, allowing anyone to think of new and powerful ways to use these approaches. The breadth of Sayre's intellectual spectrum reached far beyond crystallography. He was also a member of the IBM team that developed the original Fortran compiler, the first high-level programming tool (see http://www.ibm.com/ibm100/us/en/icons/fortran/team/ for more details). Currently, 55 years after the first commercial release of Fortran, this language is still in wide use. The history of crystallographic computing, and scientific computing in general, cannot be separated from the success of Fortran, made possible by the amazing IBM team that included Sayre. In spite of his great accomplishments, David Sayre was modest and approachable in person, and he was generous in sharing credit with his colleagues. He will be greatly missed. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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phenix.elbow problem
by Simon Kolstoe 12 Mar '12

12 Mar '12

Hi there, Who's the best person to talk to when phenix.elbow is not assigning correct geometry to a molecule? Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Wolfson Drug Discovery Unit University College London Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------

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error after adp refinement
by Christian Roth 10 Mar '12

10 Mar '12

Dear Phenix Team, I started a refinement with anisotropic adp and weight optimization and directly after the optimization step an error appeared which never appeared befor for me. The previous steps of mask optimization and xyz refinement worked well. Best Regards Christian AssertionError : Traceback: File "/userdata-2/christian/phenix- dev-979/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/userdata-2/christian/phenix- dev-979/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/runtime.py", line 68, in __call__ call_back_handler=callback) File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/command_line.py", line 97, in run call_back_handler=call_back_handler) File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/driver.py", line 1494, in run ncs_manager = self.ncs_manager) File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/strategies.py", line 1046, in refinement_machine h_params = h_params) File "/userdata-2/christian/phenix- dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 212, in __init__ nproc = nproc) File "/userdata-2/christian/phenix- dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 389, in __init__ compute_gradients=False).target_work()) Platform info: __FILE__ = /net/longnose/scratch2/phenix/phenix- dev-979/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Feb 7 2012 __TIME__ = 02:05:24 __i386__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 BOOST_LIB_VERSION = 1_48 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 12 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.10.1 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.31-23-generic-pae-i686-with-debian-squeeze-sid platform.architecture(): ('32bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 8 Memory total: 25,405,636,608 Memory free: 20,305,633,280 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å

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Calculating Bijvoet difference Fourier map
by John Rose 08 Mar '12

08 Mar '12

Hi, I am some what new to PHENIX and using the Mac GUI. I want to compute a Bijvoet difference Fourier map. Any help would be appreciated. John Rose

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autobuild omit map as Fo-Fc
by Ursula Schulze-Gahmen 07 Mar '12

07 Mar '12

I calculated an omit-map for my model using the following command inpt: phenix.autobuild data=HKL2000+R.mtz model=ptefb_A4_refine_43.pdb omit_region_specification=omit_around_pdb omit_box_pdb_list=G_chain.pdb composite_omit_type=refine_omit maps_only=true I would like to display a 2Fo-Fc and Fo-Fc map but I cannot find the overall_best_refine_map_coeffs.mtz output file that should have these coefficients according to the manual. I only see the overall_best_denmod_map_coeffs.mtz file. Can somebody tell how to best get to an omit Fo-Fc or 2Fo-Fc map? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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bins in phenix.refine
by Jianghai Zhu 06 Mar '12

06 Mar '12

Hi, A colleague asked me a question if phenix.refine can use user-input resolution bins for R and Rfree calculation. I am not sure if such parameters exist. -- Jianghai

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where is the fo-fc omit map?
by Yu, Hongjun 06 Mar '12

06 Mar '12

hello, It is so good that phenix can caculate sa-omit map so easily. But I am new to this. When I finish caculating, I can only get acess to 2fo-fc map whe I use coot to open the file: resolve_composite_map.mtz . How can I open the fo-fc omit map? I notice this from phenix.autobuild manual page "Note 1: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz". I don't understand this because the omit_regin.mtz seem to be the omit box I specify. Is this correlated with my problem? Any advice is appreciated. Thank you in advance! Sincerely, Hongjun

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phenix.get_cc_mtz_pdb but allow for atom selections.
by Francis E Reyes 06 Mar '12

06 Mar '12

It'd be wonderful to pass in an atom selection (say backbone, or ligand or what have you) into phenix.get_cc_mtz_pdb . Is this functionality available in some other phenix util? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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