- phenixbb - phenix-online.org

effect of solvent fraction on density modification/solvent flattening for a membrane protein
by Pascal EGEA 08 Jun '08

08 Jun '08

Dear All, This is a question about the effect of solvent fraction estimation on the quality of the initial phases. I am trying to solve the structure of a membrane protein at moderate resolution 3.5A from a MAD data set (peak, inflection and high energies). I have one copy of my complex which gives me a solvent fraction of 0.7 without considering the contribution of the detergent. With a related molecule I found a Phaser-MR solution but it does not refine although it is right. I am using Phenix with the phases obtained from molecular replacement and combining them with the MAD signal to locate the seleniums. A visual inspection of the anomalous fourier difference map shows 6 sites out of the 7 expected at 4sigma contouring. If I let Phenix decide by itself it goes on its own with two copies in the ASU and considers a solvent fraction of 0.50; then it finds 7 sites (and not 14 ? why is that?) (the seventh is weak but we expect this for this region of the complex). now if I force Phenix to take ncs_copies=1 and solvent fraction=0.7 then it only find 6 sites. Wether it is 2 "freely chosen" molecules/ASU and 0.5 of solvent or 1 "forced" molecule/ASU and 0.7 of solvent, the 6 first sites are identical (although occupancies are quite higher in the first case) Should I take into account the detergent and lower somewhat my solvent fraction (in the 0.6 range maybe) with the fixed one copy ASU estimation or just trust Solve/Resolve when it runs the density modification part. Does it really affect the quality of the phasing? Between these two extremes I am surprised to see that the quality of the resolve map are quite similar apparently showing clear new structural features. Thanks in advance for your comments, Pascal F. Egea, PhD Post Doctoral Researcher University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

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OS X source install relocatable?
by Ben Eisenbraun 05 Jun '08

05 Jun '08

Howdy, I'm doing an install from source on Mac OS X from the latest Phenix source packages. We install everything on an NFS mount so we can share it out to the workstations, so it's a little different than most OS X installs I suspect. Anyway, the installer was failing like this: (from the top level source directory) ./install --prefix=/programs/i386-mac/phenix/1.3-rc2 Which was getting me: configuring python compiling python csh: /programs/source/phenix/1.3-rc2/osx86/phenix-installer-1.3/bin/check_lib: No match. installation of python failed problem building main python library Looking at bin/install-from-source, it was failing on line 482: set py_lib = `$PHENIX_TAR/bin/check_lib $PHENIX_BUILD/base/Python.Framework/Versions/Current/lib/python*/config python` The reason for the failure is that the python framework installs with a lower case 'f': /programs/i386-mac/phenix/1.3-rc2/phenix-1.3-rc2/build/mac-intel-osx/base/Python.framework/ On a default HFS+ volume, which is case insensitive, this works just fine, but it fails when you try to install on a case-sensitive volume. Editing bin/install-from-source and :%s/Python.Framework/Python.framework/g seems to have fixed the build problem. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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constraining alpha-helical geometry in phenix
by Pascal EGEA 05 Jun '08

05 Jun '08

Dear All, I am currently refining a structure at moderate resolution (~3.4A) which is mainly composed of alpha-helices . Is there a way to constrain the backbone geometry of the alpha helical regions in the model used for refinement. Many Thanks, Pascal F. Egea, PhD Post Doctoral Researcher University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

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System Administrator Position in Berkeley California
by Paul Adams 04 Jun '08

04 Jun '08

System Administrator 3 Position =============================== The Joint BioEnergy Institute is seeking a Systems Administrator, to be a part of the Technology Division. The scope of this position includes managing scientific computing resources, primarily linux- based clusters and servers, making project and public data accessible in a timely manner to project participants, and integrating the data with existing data from other databases. The Joint BioEnergy Institute (JBEI) is a new multi-organizational research center comprising world-class resources and expertise located in one facility at Emeryville, California. The goal of JBEI is to use rapidly advancing scientific techniques, such as systems and synthetic biology, to accelerate development of the nation's biofuels industry. JBEI is a U.S. Department of Energy funded Bioenergy Research Center, managed by Lawrence Berkeley National Laboratory (LBNL) with partners from 5 internationally recognized scientific institutions: Sandia National Laboratories (SNL), Lawrence Livermore National Laboratory (LLNL), University of California-Davis (UCD), University of California- Berkeley (UCB), and the Carnegie Institution for Science Duties: Plan, organize, prioritize and complete assigned tasks and projects in a timely manner. Frequently and clearly communicate task or project status to customers to either set or negotiate expectations. Under the broad supervision of the Vice President of Technology and the Computational Analysis Director: Provide linux system administration and user support for research groups. This includes system installations, software installations from packages or from source code, distribution upgrades, OS and security patches, system monitoring, disk and file system management, system hardware and peripheral management, backup and recovery management, troubleshooting, and crash recovery. Configure, administer, and troubleshoot various compute clusters, web and database servers, and other services and daemons. Participate in the formulation, planning, organizing, implementation and support of new services or capabilities. Provide basic support for linux desktop systems, including hardware and software installations and upgrades. Support a group of approximately 10 full-time programmers and computational biologists in using JBEI computational resources. Key Success Factors: At least five years linux system administration experience, with responsibility for a wide range of hardware and distributions. Specific areas of required experience include compute cluster and job queuing software administration and support; Apache; Python/Perl; bash/ tcsh, including writing complex Bourne shell scripts; runlevel 1 for critical update or recovery purposes; remote administration, including ssh, remote serial consoles, and remote PDUs; NFS; and monitoring various models of RAID controller. Firm understanding of linux internals including the boot process, kernel versions, and recovery scenarios. Experience with a code management system, preferably CVS or Subversion, as both administrator and code contributor. Experience with relational database operation and maintenance, specifically with MySQL, PostgreSQL or Oracle. Database experience should include database design, implementation, installation, and administration, including backup and restore of large databases. Demonstrated ability to make progress on multiple tasks simultaneously, and to work both independently and as a member of a team. Must be available as needed nights and weekends for critical system updates that cannot be performed during regular lab hours. Application Procedure: This is a full-time one-year Term appointment, renewable under the same conditions, contingent upon the continued availability of funding and work. For consideration apply online at: http://jobs.lbl.gov, select "Search Jobs", and enter job number 21565 in the keyword search field. For more information about JBEI go to: www.jbei.org -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology 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. Administrator: Delia Clark [ DNClark(a)lbl.gov ][ 1-510-486-6331 ] --

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optional bits of the CCI Apps installion?
by Ben Eisenbraun 03 Jun '08

03 Jun '08

Hi Phenix Developers, When I install CCI Apps, I end up with a directory that looks like this: $ ls -1 1NSF.pdb cci_apps_build cci_apps_fedora3_py251.selfx cci_apps_install_script.csh cci_apps_sources nsf_d2_peak.sca test_apps Which of the bits are optional and can be deleted without affecting the installation? It seems like the selfx install file is fine to delete. How about the sources directory? $ du -k --max-depth=1 62584 ./cci_apps_sources 125840 ./cci_apps_build 225012 . If the sources directory is not needed, that would save me about 30% of the disk use for the installation, and since I have 2-3 concurrent versions installed, and those versions get pushed around to ~75 machines across the network, every bit I can trim helps. As a side note, I think it might be clearer to refer to the "Opteron" builds of the CCI Apps as AMD64 or x86_64. I didn't see anything on the download page that makes this explicit. Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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Group ADP not working
by alebus＠pasteur.edu.uy 03 Jun '08

03 Jun '08

Dear all, I am refining a structure (2.9angs res; P21) with phenix (Version: 1.3b; Release tag: rc6; linux platform) I want to carry on group_ADP refinement, according to the ('lengthy') command line : phenix.refine eden_unique1.hkl hlcoeff_blur.hkl abril28_phenix.pdb input.experimental_phases.labels="PA_BLUR PB_BLUR PC_BLUR PD_BLUR" ordered_solvent=false simulated_annealing=false simulated_annealing.mode=first strategy=rigid_body+individual_sites+group_adp+tls main.ncs=tru e main.number_of_macro_cycles=10 xray_data.low_resolution=15.0 xray_data.high_resolution=2.7 tls_group_selections.params rigid_body_selections.params group_anomalous_1.params elbow.acp_A_pdb.001.cif restraints_edits.params convert_to_isotropic=true everything works just fine (including correct handling of an 'unusual' ligand; selected NCS restraints; TLS; etc)...except for the group ADP : phenix keeps doing individual atom B-factor refinement (e.g. these are some pertinent remarks in the output pdb REMARK ****************** REFINEMENT STATISTICS STEP BY STEP ****************** REMARK leading digit, like 1_, means number of macro-cycle REMARK 0 : statistics at the very beginning when nothing is done yet REMARK 1_bss: bulk solvent correction and/or (anisotropic) scaling REMARK 1_xyz: refinement of coordinates REMARK 1_rbr: rigid body refinement REMARK 1_gbr: group B-factor refinement REMARK ------------------------------------------------------------------------ REMARK R-factors, x-ray target values and norm of gradient of x-ray target REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.3951 0.4346 -6.345353e+00 -6.295977e+00 REMARK 1_bss: 0.3189 0.3519 -6.182904e+00 -6.132416e+00 REMARK 1_rbr: 0.3199 0.3553 -6.164872e+00 -6.111524e+00 REMARK 1_bss: 0.3197 0.3548 -6.158236e+00 -6.106543e+00 REMARK 1_xyz: 0.3145 0.3612 -6.243414e+00 -6.163029e+00 REMARK 1_adp: 0.2890 0.3327 -6.111496e+00 -6.011406e+00 REMARK 2_bss: 0.2862 0.3290 -6.107396e+00 -6.004629e+00 REMARK 2_xyz: 0.2801 0.3278 -6.104559e+00 -5.995221e+00 REMARK 2_adp: 0.2783 0.3213 -6.062947e+00 -5.954846e+00 REMARK 3_bss: 0.2783 0.3214 -6.063301e+00 -5.955103e+00 REMARK 3_xyz: 0.2755 0.3218 -6.065099e+00 -5.950739e+00 REMARK 3_adp: 0.2751 0.3218 -6.062715e+00 -5.947567e+00 ... and so on, always doing 'X_adp' (and not 'X_gbr') on the different steps... starting from a single value on the B-factor column in the input pdb, of course I end up having individually varied figures in the end, which I don't want I will greatly appreciate any help on what am I doing wrong. Thanks, Alejandro

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phenix.elbow
by Morten Grøftehauge 02 Jun '08

02 Jun '08

Dear Phenix.BB, I wrote a mail earlier about some problems I had with phenix.elbow but it didn't seem to get through. I've solved two of the problems now but also found a new one so I'll try posting again. When you set the --xyz option along with --clean then your .xyz file is deleted. Of course the easy solution is simply to not use --clean but I imagine that it is a minor bug since it doesn't happen with --tripos. Secondly I have a slightly larger problem. When an isoSMILES with more than one molecule is inputted then phenix.elbow joins them up to a single molecule (or places them so closely that all programs, including phenix.elbow, interprets them as one molecule when converting to a format such as mol2 with explicit bonds). For an example try phenix.elbow --output=009_3085017 --write_hydrogens=false --overwrite --clean --tripos --smiles='C=CCN.C1C(O1)CCl' The period is supposed to designate two seperate molecules. Remember to use elbow.become_expert before running that line. I hope someone can help me. Sincerely, -- Morten K Grøftehauge PhD student Department of Molecular Biology Gustav Wieds Vej 10 C 8000 Aarhus C - Denmark Phone: +45 89 42 52 61 Fax: +45 86 12 31 78 www.bioxray.dk

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shell variable SSH_Path not set
by shivesh kumar 02 Jun '08

02 Jun '08

Dear all, We have installed Phenix in Red Hat Linux enterprises 5. It takes a long time for the GUI to appear with the following message-- Shell variable SSH_Path not set What is the solution of this problem. Thanx in advance for suggestions. shivesh

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Error running cci_apps
by JENDREK 29 May '08

29 May '08

Hi, I've encountered following error running cci_apps (25.05.08 build): Sorry: Error reading CIF file: "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/monomer_library/mod_rnaC2.cif" (IOError: [Errno 2] No such file or directory: '/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/monomer_library/mod_rnaC2.cif') I thought it might be my data fault but the same error appears during test_apps script. I'm running cci_apps on the Mac (Tiger 10.4.11). Funny thing that Phenix 1.3rc2 is running without the problem. I hope someone can help me solve the mystery... Andrzej -- alnyds[at]gmail[dot]com

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prosthetic group
by Bryan W. Lepore 29 May '08

29 May '08

should prosthetic groups be attached to proteins by those LINK or CONNECT records as found in typical PDB files? e-LBOW seems for _ligands_ only. -bryan

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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Cyndi Salbego 28 May '08

28 May '08

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Variable energy between 6-18keV, ADSC Q315 Detector, MAD Capable. Focused beam size 20x80micron Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV), ADSC Q315 Detector. Contact csalbego(a)anl.gov for further details. See http://necat.chem.cornell.edu for information on our beamlines and a calendar of available days.

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syntax and alternate conformations
by Mark Collins 28 May '08

28 May '08

Hi I have an unexpected result, my syntax must be incorrect. The relevant script commands are below, the problem is residues A113 and B143 have alternate conformation occupancies that sums to 0.98 to 1.06 respectively. Clearly alternate conformations of a single residue should sum to 1 (or less than 1 possibly). Any suggestions please? Thank you, Mark refine { strategy = *individual_sites \ rigid_body \ *individual_adp \ group_adp \ tls \ individual_occupancies \ *group_occupancies \ group_anomalous \ occupancies { individual = None group = chain A and resid 113 and altid A group = chain A and resid 113 and altid B group = chain B and resid 143 and altid A group = chain B and resid 143 and altid B } }

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Re: [phenixbb] problem with high Rfree
by Christina Bourne 28 May '08

28 May '08

Thank you very much for your help. I just wanted to follow up in how I'm progressing with this. I tried the things you suggested, as well as a variety of others, with no luck. It turns out that my 4mol/AU P41 twinned data is ACTUALLY 8mol/AU P212121. The packing in the AU has an almost 41 screw relating 4 mols to the other 4. When this operation is carried out, 2 mols overlay 2 others almost perfect, while the other 2 overlay the other 2 by 180 degrees. So my AU packing is a pseudo-41 with apparent twinning. (The b dimension did not need halving, so my cell is 2x the size, if that makes sense). The data refines very well as P212121, and Rfree drops like a rock. Again, thank you so much for your suggestions, and Phenix is really wonderful! Christina ----- Original Message ---- From: Pavel Afonine <pafonine(a)lbl.gov> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Sent: Tuesday, May 20, 2008 1:51:42 AM Subject: Re: [phenixbb] problem with high Rfree Hi Christina, I usually observe similar R/Rfree behavior when I use LS target instead of maximum-likelihood. In fact, twin refinement in phenix.refine is based on LS target function. This is just to share my observations; it's not necessarily happening in your case. - How many of test reflections you have and how they are distributed in resolution bins? - Just out of curiosity: did you try to ignore twinning and run refinement with default target? - What if you don't run SA? - Did you try to play with target weights (try different values for wxc_scale and wxu_scale) to see how this affect the R-factors? - Are you using the latest (or one of) phenix.refine? - Did you try to fill in water? Could you send a log file: may be we could spot something outstanding... Pavel. On 5/19/2008 1:32 PM, Christina Bourne wrote: Hello BB, I am working on a structure that is twinned (merohedral) in P41. Initial estimates of twinning fraction (via xtriage and Yeates server) are around 0.37; in refinement they start around 0.49 and drop to 0.46 (so far). My MR soln is good (Phaser LLG ~550) with 4 mols per AU; this gives good packing with no room for another mol. I have data from 48-2.8A. I should mention that data processing wasn't easy- this crystal form also has an apparent epitaxial twin in the b dimension causing a doubling in that dimension. During indexing (with SAINT) I applied a transformation of 100 00.50 001 to the reflections, which then gave me the expected cell and from Xprep the data looks OK. (Yes, I am trying to grow different forms) Maps look nice, although I wish my ligand had more/better density. I ran phenix.refine with defaults, and included twin_law="h,-k,-l", xray_data.r_free_flags.generate=true, detwin.map_types.aniso_correct=true and also simulated_annealing=true. My starting R/ Rfree is 0.448/ 0.4385; ending is 0.2962/ 0.4270. Geometry is somewhat tighter after refinement but is better (bonds 0.017 to 0.01, angles 1.966 to 1.530). I have not included my ligand, and I can see a few spots where the model needs adjusting, but nothing majorly wrong. Why is my Rfree hanging so high? Is it becaues I have bad karma? Is it to do with the twinning? I am pretty sure my space group is right (based on the above info and the maps look fine; Phaser could not find a solution in P43). There isn't room for anything else in the cell. Any opinions or suggestions are most welcome as I wait for better xtals to grow... Thanks in advance, Christina ________________________________ _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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OXT
by Rife, Christopher L 23 May '08

23 May '08

Should phenix.refine be able to handle OXT? I find it is moving the OXT atom ~2A from where it should be. Do I need to rename it or add a separate definition to the refinement? Thanks, Chris

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IUCr Crystallographic Computing School 2008
by Ralf W. Grosse-Kunstleve 23 May '08

23 May '08

IUCr Crystallographic Computing School 2008 * Sharing our knowledge * Kyoto, Japan, August 18-23 http://www.iucr.org/iucr-top/comm/ccom/kyoto2008/program.html The IUCr Crystallographic Computing School 2008 school aims to bring together both computational methods developers and users interested in looking beyond the interface. The format of the school fosters exchange of ideas via formal lectures, afternoon tutorials, coding challenges and code comparison sessions. The world-wide crystallographic community (including macro- and small-molecule crystallography, powder diffraction, and small-angle scattering) is invited to an intensive session of working together and learning from each other. The schedule of the program is available via the web link above. Abstracts are being added. Thanks to support from sponsors, we have been able to keep the registration cost (including accommodation and meals) below 70,000 YEN (ca. 430 EUR, 665 USD). The number of attendees is limited to 80 students. For more information visit the web site above. The registration deadline is July 25th, 2008. Organizing committee: A. L. Spek (Utrecht University , Netherlands) R. Grosse-Kunstleve (LBNL, USA) M. Yao (Hokkaido University, Japan) A. Nakagawa (Osaka Institute of Protein, Japan) H. Powell (MRC, UK) L. Cranswick (NRC , Canada)

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Shell variable SSH_Path not set
by shivesh kumar 23 May '08

23 May '08

Dear all, We have installed Phenix in Red Hat Linux enterprises 5. It takes a long time for the GUI to appear with the following message-- Shell variable SSH_Path not set What is the solution of this problem. Thanx in advance for suggestions. shivesh

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NCS restraints
by Rife, Christopher L 22 May '08

22 May '08

I'm refining a twinned structure at 2.2A that has 6 copies in the ASU. I am using NCS, however the ncs restraints are so tight that they are keeping the chains identical even though this takes them out of the density. Are there any parameters I can adjust that will lessen the strength of these restraints? Taking away NCS completely is also not ideal. I guess I would like an equivalent of 'medium' or 'loose' NCS restraints as implemented in Refmac. Thanks, Chris

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Re: [phenixbb] Any real space map-mask / NCS utility?
by Tom Terwilliger 22 May '08

22 May '08

Hi Partha, I think we don't have a tool for just what you want...but here is an idea given what you are trying: In coot build a short piece of polypeptide in the region where one ha site is located. Match the map in some way. Now rotate/translate this exact piece of chain over to your other sites and match the density there. Now use phenix.superpose_pdbs to find your ncs and put that in resolve. Good luck! -Tom t At 05:48 AM 5/22/2008, you wrote: >Hi, > >Apologies for the strange question. > >Since phenix has one fantastic tool for each kind of purpose, I was >wondering if there is something that could combine features of USF >Rave package for example.. basically the question arises from the >difficulty of finding NCS operators in some cases, if we have less >than three heavy atoms per molecule or map is too bad to build >something. > >I am trying to create a mask around a heavy atom site in the map, give >it a translation to the next heavy atom which is probably in the next >molecule, give a 6d rotation and use that in Resolve for NCS >averaging. > >Any suggestion / script would be greatly appreciated. > >Cheers, Partha > > >-- >MRC National Institute for Medical Research >Division of Molecular Structure >The Ridgeway, NW7 1AA, UK >Email: pchakra(a)nimr.mrc.ac.uk >Phone: + 44 208 816 2515 >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb 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.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Any real space map-mask / NCS utility?
by Partha Chakrabarti 22 May '08

22 May '08

Hi, Apologies for the strange question. Since phenix has one fantastic tool for each kind of purpose, I was wondering if there is something that could combine features of USF Rave package for example.. basically the question arises from the difficulty of finding NCS operators in some cases, if we have less than three heavy atoms per molecule or map is too bad to build something. I am trying to create a mask around a heavy atom site in the map, give it a translation to the next heavy atom which is probably in the next molecule, give a 6d rotation and use that in Resolve for NCS averaging. Any suggestion / script would be greatly appreciated. Cheers, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

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decrease number of refs in test set
by Mark A Saper 21 May '08

21 May '08

I have a data set with about 10% of the reflections in the test set. I want to retain this test set for further refinement in phenix, but I want to decrease the number of reflections to say 5%. Can this be done in phenix? Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor, Biophysics and Department of Biological Chemistry University of Michigan 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 Research summary

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phenix.twin_map_utils gives AttributeError: 'module' object has no attribute 'r_free_flags_params'
by Francis E Reyes 21 May '08

21 May '08

chem171-152-dhcp:exptl_fobs_phases_freeR_flags.mtz francisreyes$ phenix.twin_map_utils xray_data.file=exptl_fobs_phases_freeR_flags.mtz model=MR.1_pdbset1_refine_007.pdb unit_cell=73.5,73.5,114,90,90,90 space_group="P 41 21 2" twin_utils { input { unit_cell = 73.5 73.5 114 90 90 90 space_group = "P 41 21 2" xray_data { file_name = "exptl_fobs_phases_freeR_flags.mtz" obs_labels = None free_flag = None } model { file_name = "MR.1_pdbset1_refine_007.pdb" } } parameters { twinning { twin_law = None max_delta = 3 } } output { logfile = "twin_tools.log" map_coeffs_root = "MAP_COEFFS" obs_and_calc = "obs_and_calc.mtz" } } Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc5/mmtbx/mmtbx/command_line/ twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc5/mmtbx/mmtbx/twinning/ twin_map_utils.py", line 256, in run tmp_params = utils.r_free_flags_params.extract() AttributeError: 'module' object has no attribute 'r_free_flags_params' Any ideas? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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phaser_x.mtz, resolve_x.mtz and exptl_fobs_phases_freeR_flags.mtz give different Rfree's using same model?
by Francis E Reyes 20 May '08

20 May '08

Ok. I think I have a case where I can't refine unless I use density modified experimental phases. I did an autosol run where I specified build=False so I don't have an exptl_fobs_phases_freeR_flags.mtz, but I do have phaser_1.mtz and resolve_1.mtz. However, when I refine my model using mlhl my Rfree drops below 30 when using resolve_x.mtz and not phaser_x.mtz nor using the original d*trek ref using the same model? Using any of the other mtz's results in Rfree's in the mid 30s. Interestingly refining against the original d*trek results in an increase of Rfree with macro cycle? I checked the log file for resolve_x.mtz and although it says it's using the mlhl refinement target, it seems to be using FP, SIGFP (not the HL coefficients that I thought phased refinement would use) as evidenced by the .log file under 'Non-default parameters'. In this section it doesn't read in the HL cofficients? Is there any indication that it's actually refining against the phases? Any insight as to which mtz to use for final refinement would be suggested. Thanks FR P.S. What is the refinement target ml_sad? --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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problem with high Rfree
by Christina Bourne 20 May '08

20 May '08

Hello BB, I am working on a structure that is twinned (merohedral) in P41. Initial estimates of twinning fraction (via xtriage and Yeates server) are around 0.37; in refinement they start around 0.49 and drop to 0.46 (so far). My MR soln is good (Phaser LLG ~550) with 4 mols per AU; this gives good packing with no room for another mol. I have data from 48-2.8A. I should mention that data processing wasn't easy- this crystal form also has an apparent epitaxial twin in the b dimension causing a doubling in that dimension. During indexing (with SAINT) I applied a transformation of 100 00.50 001 to the reflections, which then gave me the expected cell and from Xprep the data looks OK. (Yes, I am trying to grow different forms) Maps look nice, although I wish my ligand had more/better density. I ran phenix.refine with defaults, and included twin_law="h,-k,-l", xray_data.r_free_flags.generate=true, detwin.map_types.aniso_correct=true and also simulated_annealing=true. My starting R/ Rfree is 0.448/ 0.4385; ending is 0.2962/ 0.4270. Geometry is somewhat tighter after refinement but is better (bonds 0.017 to 0.01, angles 1.966 to 1.530). I have not included my ligand, and I can see a few spots where the model needs adjusting, but nothing majorly wrong. Why is my Rfree hanging so high? Is it becaues I have bad karma? Is it to do with the twinning? I am pretty sure my space group is right (based on the above info and the maps look fine; Phaser could not find a solution in P43). There isn't room for anything else in the cell. Any opinions or suggestions are most welcome as I wait for better xtals to grow... Thanks in advance, Christina

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Can't autobuild after autosol?
by Francis E Reyes 19 May '08

19 May '08

******************************************************************************** Failed to carry out AutoBuild_start: Sorry, 'after_autosol' is set, but there were not any solutions from AutoSol found...please make sure that the highest-numbered AutoSol run is a completed run (you can use 'phenix.autosol show_runs' to see what runs are present and 'phenix.autosol delete_runs=xx' to remove any incomplete runs) ******************************************************************************** when issues with phenix.autobuild after_autosol phenix.autosol show_runs gives.. ------------------------------------------------------------ Starting AutoSol with the command: phenix.autosol display_runs=True --------------------------------------------------------------------------- List of runs for AutoSol Run Title / Notes --------------------------------------------------------------------------- --------------------------------------------------------------------------- 3: Run 3 AutoSol Fri May 16 13:10:11 2008 STEP: finished Top solution: # 2 Dataset #1 Score: 27.84 FOM: 0.29 Built: 121 Side-chains: 0 Chains: 21 CC: 0.45 Sites: 4 Score type: CC RFACTOR SKEW FOM NCS_OVERLAP Raw scores: 0.61 0.59 0.03 0.30 0.00 Z-scores: 14.84 5.76 1.26 5.98 0.00 --------------------------------------------------------------------------- Does that mean an autosol run has completed? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 3

Tell phenix.autosol to find more heavy atoms?
by Francis E Reyes 19 May '08

19 May '08

I have a SAD map which is beautiful, but I want to look for more heavy atoms before further refinement... Would the proper procedure be.... SAD dataset, reading heavy-atom sites from a PDB file written by phenix.hyss: phenix.autosol 11 Pb data=deriv.sca seq_file=seq.dat \ sites_file=deriv_hyss_consensus_model.pdb This will carry out the usual structure solution process, but will read sites from deriv_hyss_consensus_model.pdb, try both hands, and carry on from there. If you know the hand of the substructure, you can fix it with have_hand=True. Would there be a PDS friendly way to do this (not necessary though) ? i.e. phenix.autobuild after_autosol --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 1

Problem starting TLS refinement
by Jendrek 16 May '08

16 May '08

Hi, I would like to do TLS but every time I try to start it I get following error: File "/usr/local/cci_apps/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 "/usr/local/cci_apps-1421/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 69, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/cci_apps-1421/cci_apps_sources/phenix/phenix/refinement/driver.py", line 199, in __init__ value = 0.0) File "/usr/local/cci_apps-1421/cci_apps_sources/mmtbx/mmtbx/tls/tools.py", line 735, in generate_tlsos origins.append(xrs.center_of_mass()) File "/usr/local/cci_apps-1421/cci_apps_sources/cctbx/cctbx/xray/structure.py", line 943, in center_of_mass return self.sites_cart().mean_weighted(weights=atomic_weights) RuntimeError: mean_weighted() argument is an empty array I've attached my input file. Any suggestions on what I'm doing wrong would be greatly appreciated. Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[(a)]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND TEL.: 358 9 191 58955 FAX : 358 9 191 59940 # Default parameters for subsequent refinement # Date 2008-05-16 Time 18:33:47 EEST +0300 (1210952027.81 s) # Command to extract only non-defaults: # phenix.refine --diff-params "h135d-mg_007.def" refinement { crystal_symmetry { unit_cell = 70.31999969 173.0200043 54.97000122 90 90 90 space_group = "P 21 21 2" } input { pdb { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/h135d-mg_006.pdb" } neutron_data { ignore_xn_free_r_mismatch = False file_name = None labels = None high_resolution = None low_resolution = None outliers_rejection = True sigma_fobs_rejection_criterion = 0 sigma_iobs_rejection_criterion = 0 ignore_all_zeros = True force_anomalous_flag_to_be_equal_to = None r_free_flags { file_name = None label = None test_flag_value = None disable_suitability_test = False ignore_pdb_hexdigest = False ignore_r_free_flags = False generate = False fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True } } xray_data { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/3844_refine_data.mtz" labels = "I-obs,SIGI-obs" high_resolution = None low_resolution = None outliers_rejection = True sigma_fobs_rejection_criterion = 0 sigma_iobs_rejection_criterion = 0 ignore_all_zeros = True force_anomalous_flag_to_be_equal_to = None r_free_flags { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/3844_refine_data.mtz" label = "R-free-flags" test_flag_value = 1 disable_suitability_test = False ignore_pdb_hexdigest = False ignore_r_free_flags = False generate = False fraction = 0.05 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True } } experimental_phases { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/3844_refine_data.mtz" labels = "HLA,HLB,HLC,HLD" } monomers { file_name = None } symmetry_safety_check = *error warning } output { prefix = "h135d-mg" serial = 7 serial_format = "%03d" write_eff_file = True write_geo_file = True write_def_file = True export_final_f_model = mtz cns write_maps = True write_map_coefficients = True } electron_density_maps { map_format = *xplor map_coefficients_format = *mtz phs suppress = None map { mtz_label_amplitudes = None mtz_label_phases = None likelihood_weighted = None obs_factor = None calc_factor = None } map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 } anomalous_difference_map { mtz_label_amplitudes = "ANOM" mtz_label_phases = "PHANOM" } grid_resolution_factor = 0.3333333333 region = *selection cell atom_selection = None atom_selection_buffer = 3 apply_sigma_scaling = True apply_volume_scaling = False } refine { strategy = *individual_sites rigid_body *individual_adp group_adp *tls \ occupancies group_anomalous sites { individual = None rigid_body = "chain A" rigid_body = "chain B" } adp { individual { isotropic = all anisotropic = None } group = None one_adp_group_per_residue = True tls = "(chain A and resid 030:060)" tls = "(chain A and resid 061:135)" tls = "(chain A and resid 136:165)" tls = "(chain A and resid 166:190)" tls = "(chain A and resid 191:244)" tls = "(chain A and resid 245:307)" tls = "(chain A and resid 308:328)" tls = "(chain A and resid 329:375)" tls = "(chain B and resid 030:060)" tls = "(chain B and resid 061:135)" tls = "(chain B and resid 136:165)" tls = "(chain B and resid 166:190)" tls = "(chain B and resid 191:244)" tls = "(chain B and resid 245:307)" tls = "(chain B and resid 308:328)" tls = "(chain B and resid 329:375)" } occupancies { individual = None group = None one_occupancy_group_per_residue = False } anomalous_scatterers { group { selection = None f_prime = 0 f_double_prime = 0 refine = *f_prime *f_double_prime } } } main { bulk_solvent_and_scale = True simulated_annealing = False ordered_solvent = False ncs = False ias = False number_of_macro_cycles = 3 max_number_of_iterations = 12 use_form_factor_weights = False tan_u_iso = False use_convergence_test = False target = ml *mlhl ml_sad ls min_number_of_test_set_reflections_for_max_likelihood_target = 50 max_number_of_resolution_bins = 30 reference_xray_structure = None use_experimental_phases = None compute_optimal_errors = False random_seed = 3326496 scattering_table = wk1995 it1992 *n_gaussian neutron use_normalized_geometry_target = True target_weights_only = False use_f_model_scaled = False max_d_min = 0.25 fake_f_obs = False optimize_mask = False occupancy_max = 1 occupancy_min = 0.1 stir = None rigid_bond_test = False show_residual_map_peaks_and_holes = True fft_vs_direct = False outliers_rejection = True find_and_add_hydrogens = False } modify_start_model { selection = None adp { selection = None randomize = None set_b_iso = None convert_to_isotropic = None convert_to_anisotropic = None shift_b_iso = None scale_adp = None } sites { selection = None shake = None translate = "0" "0" "0" rotate = "0" "0" "0" euler_angle_convention = *xyz zyz } occupancies { randomize = False set = None } output { file_name = None } random_seed = None } fake_f_obs { k_sol = 0 b_sol = 0 b_cart = "0" "0" "0" "0" "0" "0" scale = 1 structure_factors_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 0.3333333333 quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } mask { solvent_radius = 1.11 shrink_truncation_radius = 0.9 grid_step_factor = 4 verbose = 1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True } scattering_table = wk1995 it1992 *n_gaussian neutron } hydrogens { refine_sites = individual *riding refine_adp = one_b_per_residue *one_b_per_molecule individual refine_occupancies = one_q_per_residue *one_q_per_molecule individual contribute_to_f_calc = True xh_bond_distance_deviation_limit = 0 build { map_type = "mFobs-DFmodel" map_cutoff = 2 angular_step = 3 use_sigma_scaled_maps = True resolution_factor = 0.25 map_next_to_model { min_model_peak_dist = 0.7 max_model_peak_dist = 1.05 min_peak_peak_dist = 1 use_hydrogens = False } max_number_of_peaks = None peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1 } } } group_b_iso { number_of_macro_cycles = 3 max_number_of_iterations = 25 convergence_test = False run_finite_differences_test = False } adp { iso { max_number_of_iterations = 25 automatic_randomization_if_all_equal = True scaling { scale_max = 3 scale_min = 10 } } } tls { one_residue_one_group = None refine_T = True refine_L = True refine_S = True number_of_macro_cycles = 2 max_number_of_iterations = 25 start_tls_value = None run_finite_differences_test = False eps = 1e-06 } adp_restraints { iso { use_u_local_only = False sphere_radius = 5 distance_power = 1.69 average_power = 1.03 wilson_b_weight_auto = False wilson_b_weight = None plain_pairs_radius = 5 refine_ap_and_dp = False b_iso_max = None } } group_occupancy { number_of_macro_cycles = 3 max_number_of_iterations = 25 convergence_test = False run_finite_differences_test = False } group_anomalous { number_of_minimizer_cycles = 3 lbfgs_max_iterations = 20 number_of_finite_difference_tests = 0 } rigid_body { mode = *first_macro_cycle_only every_macro_cycle target = ls_wunit_k1 ml *auto target_auto_switch_resolution = 6 refine_rotation = True refine_translation = True max_iterations = 25 bulk_solvent_and_scale = True euler_angle_convention = *xyz zyz lbfgs_line_search_max_function_evaluations = 10 min_number_of_reflections = 100 multi_body_factor = 1 zone_exponent = 4 high_resolution = 3 max_low_high_res_limit = None number_of_zones = 5 } ncs { find_ncs { temp_dir = "" min_length = 10 njump = 1 njump_recursion = 10 min_length_recursion = 50 min_percent = 95 max_rmsd = 2 quick = True max_rmsd_user = 3 domain_finding_parameters { find_invariant_domains = True initial_rms = 0.5 match_radius = 2 similarity_threshold = 0.75 smooth_length = 0 min_contig_length = 3 min_fraction_domain = 0.2 max_rmsd_domain = 2 } verbose = False } find_automatically = True coordinate_sigma = None b_factor_weight = None excessive_distance_limit = None special_position_warnings_only = False restraint_group { reference = None selection = None coordinate_sigma = 0.05 b_factor_weight = 10 } restraint_group { reference = "chain A and (resseq 30:374 )" selection = "chain B and (resseq 30:374 )" coordinate_sigma = 0.05 b_factor_weight = 10 } } pdb_interpretation { apply_cif_modification { data_mod = None residue_selection = None } apply_cif_link { data_link = None residue_selection_1 = None residue_selection_2 = None } link_distance_cutoff = 3 disulfide_distance_cutoff = 3 chir_volume_esd = 0.2 peptide_link { cis_threshold = 45 discard_psi_phi = True omega_esd_override_value = None } nonbonded_distance_cutoff = None default_vdw_distance = 1 min_vdw_distance = 1 nonbonded_buffer = 1 vdw_1_4_factor = 0.8 translate_cns_dna_rna_residue_names = None clash_guard { nonbonded_distance_threshold = 0.5 max_number_of_distances_below_threshold = 100 max_fraction_of_distances_below_threshold = 0.1 } } geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = None atom_selection_2 = None symmetry_operation = None distance_ideal = None sigma = None } angle { action = *add delete change atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None angle_ideal = None sigma = None } } geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } ordered_solvent { low_resolution = 2.4 mode = auto filter_only *every_macro_cycle output_residue_name = "HOH" output_chain_id = "W" output_atom_name = "O" b_iso_min = 1 b_iso_max = 80 anisotropy_min = 0.1 b_iso = None scattering_type = "O" occupancy_min = 0.1 occupancy_max = 1 occupancy = 1 primary_map_type = "mFobs-DFmodel" primary_map_cutoff = 3.2 secondary_map_type = "2mFobs-DFmodel" secondary_map_cutoff = 1.2 h_bond_min_mac = 1.2 h_bond_min_sol = 1.2 h_bond_max = 3.2 new_solvent = *isotropic anisotropic refine_adp = True refine_occupancies = False filter_at_start = True n_cycles = 3 ignore_final_filtering_step = False } peak_search { use_sigma_scaled_maps = True resolution_factor = 0.25 map_next_to_model { min_model_peak_dist = 1.8 max_model_peak_dist = 6 min_peak_peak_dist = 1.8 use_hydrogens = False } max_number_of_peaks = 5232 peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1.8 } } bulk_solvent_and_scale { bulk_solvent = True anisotropic_scaling = True k_sol_b_sol_grid_search = True minimization_k_sol_b_sol = True minimization_b_cart = False target = *ls_wunit_k1 ml symmetry_constraints_on_b_cart = True k_sol_max = 0.6 k_sol_min = 0 b_sol_max = 150 b_sol_min = 0 k_sol_grid_search_max = 0.6 k_sol_grid_search_min = 0 b_sol_grid_search_max = 80 b_sol_grid_search_min = 20 k_sol_step = 0.3 b_sol_step = 30 number_of_macro_cycles = 2 max_iterations = 25 min_iterations = 25 fix_k_sol = None fix_b_sol = None fix_b_cart { b11 = None b22 = None b33 = None b12 = None b13 = None b23 = None } apply_back_trace_of_b_cart = False verbose = -1 ignore_bulk_solvent_and_scale_failure = False } alpha_beta { free_reflections_per_bin = 140 number_of_macromolecule_atoms_absent = 225 n_atoms_included = 0 bf_atoms_absent = 15 final_error = 0 absent_atom_type = "O" method = *est calc estimation_algorithm = *analytical iterative verbose = -1 interpolation = False fix_scale_for_calc_option = None number_of_waters_absent = 613 sigmaa_estimator { kernel_width_free_reflections = 100 kernel_on_chebyshev_nodes = True number_of_sampling_points = 20 number_of_chebyshev_terms = 10 use_sampling_sum_weights = True } } mask { solvent_radius = 1.11 shrink_truncation_radius = 0.9 grid_step_factor = 4 verbose = -1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True } cartesian_dynamics { temperature = 300 number_of_steps = 200 time_step = 0.0005 initial_velocities_zero_fraction = 0 n_print = 100 verbose = -1 } simulated_annealing { start_temperature = 5000 final_temperature = 300 cool_rate = 100 number_of_steps = 25 time_step = 0.0005 initial_velocities_zero_fraction = 0 interleaved_minimization { number_of_iterations = 0 time_step_factor = 10 restraints = *bonds *angles } n_print = 100 update_grads_shift = 0.3 refine_sites = True refine_adp = False max_number_of_iterations = 25 mode = every_macro_cycle *second_and_before_last once first verbose = -1 } target_weights { wxc_scale = 0.5 wxu_scale = 1 wc = 1 wu = 1 fix_wxc = None fix_wxu = None optimize_wxc = False optimize_wxu = False shake_sites = True shake_adp = 10 regularize_ncycles = 50 verbose = 1 wnc_scale = 0.5 wnu_scale = 1 rmsd_cutoff_for_gradient_filtering = 3 } ias { b_iso_max = 100 occupancy_min = -1 occupancy_max = 1.5 ias_b_iso_max = 100 ias_b_iso_min = 0 ias_occupancy_min = 0.01 ias_occupancy_max = 3 initial_ias_occupancy = 1 build_ias_types = L R B BH use_map = True build_only = False file_prefix = None peak_search_map { map_type = *Fobs-Fmodel mFobs-DFmodel grid_step = 0.25 scaling = *volume sigma } } ls_target_names { target_name = *ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed \ ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit \ ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed \ ls_wff_k1ask3_fixed lsm_kunit lsm_k1 lsm_k2 lsm_k1_fixed \ lsm_k1ask3_fixed } twinning { twin_law = None detwin { mode = algebraic proportional *auto map_types { twofofc = *two_m_dtfo_d_fc two_dtfo_fc fofc = *m_dtfo_d_fc gradient m_gradient aniso_correct = False } } } structure_factors_and_gradients_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 0.3333333333 quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } r_free_flags { fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True } }

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COURSE ANNOUNCEMENT - BIOCRYS 2008
by Daniele de Sanctis 15 May '08

15 May '08

On behalf of the organizers, Maria Armenia Carrondo and Thomas R. Schneider COURSE ANNOUNCEMENT - BIOCRYS 2008 Fundamentals of Modern Methods in Biocrystallography - 'What you always wanted to know about crystallography but never dared to ask' http://biocrys.itqb.unl.pt 4th - 11th October 2008 at the Instituto de Tecnologia Química e Biológica, Oeiras, Portugal. The topics of the second edition of this course will run from fundamentals such as symmetry, point groups and crystal systems, basic diffraction physics, reciprocal space and the Ewalds sphere, radiation damage, data processing, structure factors, Patterson function to modern methodologies including molecular replacement, SAD, MAD, MIR and maximum likelihood phasing, density modification, refinement, model building, twinning and structure validation. The course will be organized with lectures in the mornings and interactive practicals and tutorials in the afternoons. Evening lectures on current topics will be presented by the invited speakers. Instructors and speakers (confirmed): M. Archer, I. Bento, N. Berrow, G. Bunkoczi, M. Coll, K. Cowtan, Z. Dauter, D. de Sanctis, P. Donner, C. Frazão, E. Garman, C. Hermes, E. Hough, G. Leonhard, A. Leslie, P. Matias, A. Perrakis, T. Schneider, C. Vonrhein. 36 participants will be selected with preference to scientists at the beginning of their crystallographic career and to those from Europe. Registration fee is 500 Eur and a fee of 700 Eur is requested for full board and accommodation. Selected applicants will have to pay the registration fee by bank transfer before arrival. A very limited number of grants may be available to partially cover the registration fees and will be paid upon students arrival. For application, please please fill the form on the web page http://www.embl-hamburg.de/workshops/2008/BIOCRYST08/ by the 15th of July For more information visit the course web page http://biocrys.itqb.unl.pt -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartado 127 2781-901 Oeiras Portugal

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User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 May '08

14 May '08

Dear Users, The Berkeley Center for Structural Biology (BCSB) is pleased to announce the launch of a Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists will be able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the egular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects 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 submit a proposal, go to: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for July/August, 2008, proposals must be submitted by May 15, 2008. The deadline for CC proposals for the time period September/October 2008 is July 15, 2008. Regards, Banumathi Sankaran

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Fixing waters around metal atom
by Jendrek 14 May '08

14 May '08

Hi, I have a structure with a metal beautifully coordinated by 3 water molecules. However, every time I run phenix.refine water picking they get removed (probably due to combination of being too close to metal/too deep in the density). So far I've been manually reentering them into pdb but it becomes a bit frustrating. Is there a way to fix those waters during water picking? Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[(a)]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND TEL.: 358 9 191 58955 FAX : 358 9 191 59940

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Beamtime available; Deadline for applications : May 15.
by Peter Zwart 12 May '08

12 May '08

Dear All, The Berkeley Center for Structural Biology (BCSB) has recently completed a major upgrade of the Sector 5.0 beamline optics. A five- to tenfold improvement in available flux has been achieved at the side-station beamlines (5.0.1 and 5.0.3), which now generate 1.5x10^11 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. The performance of 5.0.2 (a tunable beamline) has improved by a factor of 3 to 4. It now generates a peak flux of 8x10^11 photons per second under typical user operations. The upgrade has also extended the energy range of 5.0.2 to 16 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. All the BCSB beamlines have robotic sample changers. The sector 5 beamlines are equiped with Berkeley Automounters (BAMs). The tuneable beamlines 8.2.1 and 8.2.2 are now equiped with Actor sample changers. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to take advantage of the upgrades to these BCSB beamlines, submit a General User proposal by May 15, 2008 in order to be considered for the July-August schedules at the Advanced Light Source. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. If you have any questions or would like to request open beamtime, please e-mailing BCSBBeamtime(a)lbl.gov. (Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime.) Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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B factor
by Jianghai Zhu 11 May '08

11 May '08

Hi, When TLS is used, phenix.refine gives 6 ANISOU B factors for each atoms. But we also get a number at the normal isotropic B factor position. If that number is the isotropic B factor, how was it calculated? Did you use something like the following? Uiso(e)^2=U11*e1^2+U22*e2^2+U33*e3^2+2U12*e1e2+2U13*e1e3+2U23*e2e3 Is it the same as the output from tslanl if using refmac5? -- Jianghai

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GRC on Diffraction Methods in Structural Biology
by Andrew Leslie 09 May '08

09 May '08

There is still time to apply to attend this GRC, relevant to researchers interested in Methods Development - details below! The official closing date is 22nd June, but places are limited to a total of 125. Best wishes Elspeth Garman and Andrew Leslie Gordon Research Conference on Diffraction Methods in Structural Biology July 13-18, 2008, Bates College, Lewiston, Maine, USA Co-Chairs: Elspeth Garman & Andrew Leslie The 2008 Gordon Research Conference on Diffraction Methods in Structural Biology will encompass advances in the methodology for macromolecular X-ray crystallography, and other diffraction/scattering applications. The full confirmed programme and timetable for the meeting can now be found below and at: http://www.grc.org/programs.aspx?year=2008&program=diffrac as well as details on how to register (registration closes on 22nd June 2008 but attendance is limited to 125 researchers). All macromolecular crystallographers interested in Methods development are encouraged to apply. To promote a lively meeting, we hope that all participants will present a poster and contribute to the discussions. *Confirmed Program as at 8th May 2008.* *MACROMOLECULAR STRUCTURES: PUSHING THE BOUNDARIES * Discussion Leader: *Janet Smith* (University of Michigan at Ann Arbor, USA) *Jens Preben Morth* (Aarhus University, Denmark) "Structure determination of the sodium-potassium pump" *Jack Johnson* (Scripps Research Institute, USA) "Crystallography of Viral Maturation Intermediates: Large Unit Cells, Particle Dynamics, and Energy Landscapes" *EXPERIMENTAL ASPECTS* Discussion Leader: *James Holton* (University of California, Berkeley, USA) *Douglas Juers* (Whitman College, USA) "Rational approaches to cryo-crystallography protocols" *Zbyszek Dauter* (Frederick Cancer Institute, USA) "A thoughtful approach to data collection" *Eddie Snell* (Hauptman-Woodward Medical Research Institute, USA) "Are X-rays damaging to structural biology? A case study with xylose isomerase" *Martin Weik* (Institut de Biologie Structurale, Grenoble, France) "Temperature-controlled cryo-crystallography to study the structural dynamics of proteins" *COMPLEMENTARY TECHNIQUES* Discussion Leader: *Peter Kuhn* (Scripps Research Institute, USA) *Junko Yano* (Lawrence Berkeley National Laboratory, USA) "Combination of XAS and XRD for studying a high-resolution structure of the photosynthetic water-splitting catalyst" *Dean Myles* (Oak Ridge National Laboratory USA) "New opportunities for neutron structural biology" *Carrie Wilmot* (University of Minnesota, USA) "Single crystal spectroscopy coupled to crystallography" *FUTURE DIRECTIONS IN SYNCHROTRON BASED MACROMOLECULAR CRYSTALLOGRAPHY * Discussion Leader: *Elizabeth Duke* (Diamond Light Source, UK) *Soichi Wakatsuki* (KEK, Japan) "Microfocus and low energy PX developments looking towards next generation synchrotron sources" *Ed Mitchell* (ESRF, Grenoble, France) "Bigger, better, faster, more: The ESRF Upgrade Programme" *Aina Cohen* (SSRL, USA) "Automation, Robotics and Remote Access at the SSRL Protein Crystallography Beam Lines" *Frank von Delft* (Structural Genomics Consortium, Oxford, UK) "A User's Wish: An Experiment-Focussed Beamline Interface" *EMERGING TECHNOLOGIES* Discussion Leader: *Andrew Leslie* (MRC-LMB, Cambridge, UK) *Robert F. Fischetti* (GM/CA-CAT, Argonne National Laboratory, USA) "Where have all the photoelectrons gone?" *Clemens Schulze-Briese* (Swiss Light Source, Villigen, Switzerland) "PILATUS 6M - the first year of regular user operation" *COMPUTATIONAL METHODS* Discussion Leader: *Airlie McCoy* (University of Cambridge, UK) *Sasha Popov* (ESRF, Grenoble, France) "BEST SAD data collection" *Paul Adams* (Lawrence Berkeley Laboratory, USA) "Automated structure solution with PHENIX" *Kevin Cowtan* (University of York, UK) "The 3 R's of automated model building: R-factors, resolution, and refinement" *George Phillips* (University of Wisconsin-Madison, USA) "Interpretation of electron density maps from protein crystals" *CHALLENGING PROBLEMS / MEMBRANE PROTEINS * Discussion Leader: *Tom Terwilliger* (Los Alamos National Laboratory, USA) *Chris Tate* (LMB-MRC Cambridge, UK) "Thermostabilisation and structure determination of a beta1 adrenergic receptor" *Mike Lawrence* (The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia) "Pursuit of the structure of the human insulin receptor ectodomain" *Mark Mayer* (NIH, Bethesda, USA) "Structure and function of allosteric ion binding sites in glutamate receptor ligand binding domains" *TALKS SELCETCED FROM POSTERS* *VALIDATION* Discussion Leader: *Ana Gonzales* (Stanford Synchrotron Radiation Laboratory, USA) *Gerard Kleywegt* (University of Uppsala, Sweden) "Validation" *Jane Richardson* (Duke University, USA) "MolProbity Progress: RNA, Auto-corrections, and H redux" *IMAGING METHODS OF THE FUTURE* Discussion Leader: *Raimond Ravelli* (Leiden University Medical Centre, The Netherlands) *Steve Ludtke* (Baylor College of Medicine, Houston, USA) "Resolution and Molecular Motion, Frontiers in CryoEM" *Carolyn Larabell* (Lawrence Berkeley National Laboratory) TBA

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Re: [phenixbb] mtz test set
by Ralf W. Grosse-Kunstleve 02 May '08

02 May '08

Hi Mark, > yes. however arp/warp has lost this ability in the ccp4i "classic" > mode. Oh, too bad. I wrote a small mtz_free_flipper.py script that will be part of the next CCI Apps maintenance release (hopefully tomorrow). If you want to use it right now, get the current cctbx bundle from here: http://cci.lbl.gov/cctbx_build/all.html Build tag: 2008_05_02_0119 (or later) Pick a bundle from the "cctbx+Python" column. You can install it anywhere, e.g. in /var/tmp/junk. After the perl cctbx*.selfx command is finished (a few seconds), source the setpaths script for your shell as usual, then run this command: cctbx.python cctbx_sources/iotbx/iotbx/examples/mtz_free_flipper.py your.mtz It will write a file free_flipped_your.mtz. The script assumes the R-free flags column label is "R-free-flags". If your label is different, copy the example script, modify the label (should be obvious) and run the modified script: cctbx.python copy_of_mtz_free_flipper.py your.mtz Note: the script will not work with the current CCI Apps because I had to add something to the mtz module last night to keep the script simple. Ralf

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model bias: phaser + prime-and-switch VS simulated annealing in phenix VS simulated annealing in cns + prime and switch
by hari jayaram 02 May '08

02 May '08

First off sorry for the cross post across bbs I have a molecular replacement solution for a single site mutant for data that goes out to 2.8 A. After molecular replacement in phaser I run the following and examine the maps for bias from the model. Option1: simluated annealing refinement in phenix using the phaser mtz Option2: take the phaser mtz and then just run prime and switch in resolve and look at the map Option3: First part: take the phaser mtz and then run simulated annealing and sigmaa in cns 1.2.2 . Second part: Run prime-and-switch using part1s model phases and modified Fs I am observing that Option 1 and Option 2 the maps are indistinguishable from each other and show very little bias from the model. In Option 3 just cns simulated annealing does not go as far at removing bias as cns simulated annealing plus prime-and-switch. Although my estimate of model bias is just a "look and see" feeling. Since I lack a thorough understanding of the relative merits of these algorithms I have the following questions 1)Does simulated annealing refinement as implemented in phenix use a prime-and-switch style approach to modify phases at any point to guide the refinement 2) Am I wrong in assuming that just simulated annealing and sigma-aa weighted maps for cns (Option 3 part 1) are not as good as cns simulated annealing + sigmaa+ prime_and_switch ( option3 part 2) Hoping to get a better idea on how well these approaches fair at removing model bias Hari Jayaram Postdoc , Brandeis University

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pseudo-translational symmetry refinement
by a a 01 May '08

01 May '08

Dear all: We have a set of crystal data having psuedo-translational symmetry when examined with xtriage: ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - <I^2>/<I>^2 : 2.519 - <F>^2/<F^2> : 0.724 - <|E^2-1|> : 0.854 - <|L|>, <L^2>: 0.504, 0.337 Multivariate Z score L-test: 1.854 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. No (pseudo)merohedral twin laws were found. Patterson analyses - Largest peak height : 67.742 (corresponding p value : 4.897e-06) The analyses of the Patterson function reveals a significant off-origin peak that is 67.74 % of the origin peak, indicating pseudo translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo translational symmetry is equal to the 4.8972e-06. The detected tranlational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. ------------------------------------------------------------------------------- The structure was solved by auto-sad at 2.7A. However, the r-factor can not be lowered by phenix.refine (TLS+ADP+rigid). Is there any manipuliations we can do to deal with this situation? Thanks, Zhiyong Ren, MD Anderson Cancer Center ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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mtz test set
by Mark Collins 01 May '08

01 May '08

Hi Everyone, How can I get foo.mtz in which the test set number for R-free is 0 and the working set is say 1. Thanks Mark

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autosol output to electron density figure in pymol
by shivesh kumar 01 May '08

01 May '08

Dear all, I have an overall_best.pdb and overall_best_refine_map_coeffs.mtz file as an output file from Autosol.When I open this in coot I see the nice density.How can make a figure with density using pymol.Thanx in advance for the suggestions. Shivesh

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Re: [phenixbb] native Patterson peak
by Peter Zwart 01 May '08

01 May '08

31 is not too bad actually. When you have such a PT peak, I would consider only an even number of copies in the ASU. When entering desperate mode, I would try all possible P2x2y2z flavors even though your systematic absences might be clear. Of course, experimental phases could be a good solution. HTH P 2008/5/1 David Garboczi <dgarboczi(a)niaid.nih.gov>: > We have datasets measured on crystals of a 19 kD protein that are > P212121, with cell constants of 66, 75, 136. > > Matthew's considerations say 3, 4, or 5 copies per au are probable. > > xtriage finds a native peak at (0.0, -0.5, 0.036) that is 31 in > height (origin=100) > > No self-rotation function peaks in xprep, that I can understand. > > Is this clearly translational symmetry that is making MR difficult? > > Hints as to how to go forward are welcome. > > thanks, > > Dave > > > -- > David N. Garboczi, PhD > Phone: 301-496-4773 > Investigator, Structural Biology Section (SBS) > Laboratory of Immunogenetics (LIG) > National Institute of Allergy and Infectious Diseases (NIAID) > National Institutes of Health (NIH) > Twinbrook 2/Room 110 > 12441 Parklawn Drive > Rockville, Maryland 20852-1742 > Fax: 301-402-0284 > Email: dgarboczi(a)niaid.nih.gov > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Re: [phenixbb] [ccp4bb] Need Solve/Resolve advice [shameless crosspost to phenixbb]
by Peter Zwart 30 Apr '08

30 Apr '08

Hi, (sorry for the crosspost / jumping between bb's), but I don't like advertising phenix on the ccp4bb. If new to Solve (or old as well), try using phenix.autosol. The gui is relatively intuitive, the command line (at least for SAD) as simple as possible and the documentation is very thorough. Before running autosol, try running xtriage and find out if you have translational pseudo symmetry. If you have more then a single molecule in the ASU, there will be NCS, unless all molecules have *extremely* different conformations. The NCS might not be proper/closed though. HTH Peter 2008/4/30 Megan Guelker <megdg(a)rice.edu>: > CCP4bb subcribers, > > I am a new user to Solve/Resolve and am using it on a Mad dataset. Solve > outputs three sites: > > pdb coordinates fractional coordinates > -15.833 35.392 38.440 0.0486 0.4315 0.1615 > 7.834 76.449 38.475 0.5487 0.9320 0.1617 > 16.310 60.866 37.449 0.5432 0.7420 0.1574 > > I noticed that the fractional coordinates for the first two sites are > separated by 0.5 units in x and y, and they appear to be the same site from > looking at the density surrounding them. I know that Solve can output some > sites with repetition if they are results from different seeds. > > I have tried running Solve again with ADDSOLVE and these sites as input (all > three and combinations of the three) and have not been able to pull out any > additional sites. I have also tried using various resolution ranges for > Solve. The same three sites are always output. > > The FOM for the map produced by Solve is 0.45. Resolve improves the FOM to > 0.66. > > The protein has 148 aa with 4 Se sites per protein. The crystals are in > space group P3221, and there are six copies per asymetric unit. There is no > non-crystallographic symmetry. > > I am a new user to Solve, and haven't been able to find an explanation for > why the output sites are so similar and separated by 0.5 units. Does anyone > have any experience with this type of result? I would appreciate any input > and suggestions on how to locate additional sites. > > Thank you for your consideration, > Megan Guelker > > -- > Megan Guelker > Graduate Student > Rice University > Department of Biochemistry & Cell Biology > 6100 Main St. - MS 140 > Houston, TX 77005 > 713-348-2492 (lab) > megdg(a)rice.edu > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Refining low resolution structure
by Humberto Pereira 29 Apr '08

29 Apr '08

Dear all I was trying to refining a low resolution structure with Phenix. The crystal belongs to the SG P6122 with one monomer per ASU. The monomer contains approximately 270 residues. There isn't any NCS operators. The crystal diffracts up to 4.0 Angstrons, with good statistics, however I have only 4204 unique reflections. I solved the structure by MR by Phaser and the solution was quite reasonably. Initially I performed a phenix refining cicle with SA + rigid body, however the Rs values is very divergent (43 and 59%), so I decided to use the key xray_data.r_free_flags.ignore_r_free_flags=true in order to save my precious reflections with and without SA, and I also use the group_adp., in those cases the R is about 39-40%. I want a help to decide the best refinement strategies for low resolution refinement with phenix. BTW I'm trying to produce some different constructions of the gene, expecting improve the resolution. Thanks Humberto

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

29 Apr '08

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

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

23 Apr '08

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

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twinning analysis
by Andreas Förster 23 Apr '08

23 Apr '08

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

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NCS problem
by Bobby Huether 22 Apr '08

22 Apr '08

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

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

22 Apr '08

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

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Re: [phenixbb] Phenix on Altix 350 ?
by Sankar Narayanan Manicka 20 Apr '08

20 Apr '08

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

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random seed to phenix.reflection_file_converter
by iulek＠interponta.com.br 18 Apr '08

18 Apr '08

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

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

18 Apr '08

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

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

16 Apr '08

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

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

14 Apr '08

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

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