- phenixbb - phenix-online.org

xtriage crash - what to do?
by Martin Moche 09 Jun '08

09 Jun '08

Dear Phenix developers, I got a crash when running phenix xtriage on a mtz-file in P3112. Error message below: The logfile prior to the crash is attached. Best regards, Martin ############# Error message ################ Traceback (most recent call last): File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/command_line/xtriage.py", line 7, in <module> xtriage.run(args=sys.argv[1:]) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/xtriage.py", line 725, in run plot_out = string_buffer ) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/xtriage.py", line 383, in __init__ additional_parameters=self.params.scaling.input.parameters.misc_twin_parameters) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/twin_analyses.py", line 2380, in __init__ out=out, verbose=verbose) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/twin_analyses.py", line 425, in __init__ self.show(out) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/twin_analyses.py", line 596, in show self.suggest_new_space_groups(out=out) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/twin_analyses.py", line 450, in suggest_new_space_groups tmp_space_group = sgtbx.space_group_info( str(tmp_space_group), space_group_t_den=t_den) File "/net/fileserver/xtal/phenix-1.3b-rc4/cctbx/cctbx/sgtbx/__init__.py", line 61, in __init__ space_group_symbols=symbols, t_den=space_group_t_den) RuntimeError: cctbx Internal Error: /net/longnose/scratch1/phenix/phenix-1.3b-rc4/cctbx/sgtbx/change_of_basis_op.cpp(70): CCTBX_ASSERT(c_.t().den() % s.t().den() == 0) failure. __________________________________________________ Martin Moche, Ph.D., M.Sc. Senior scientist Karolinska Institutet MBB/SGC Scheeles väg 2 171 77 Stockholm Sweden Phone: +46-8-524 868 43 Mob: +46-733-229327 Fax: +46-8-524 868 68 Martin.Moche(a)ki.se

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disulfides and .defs, maybe custom geom.
by Bryan W. Lepore 09 Jun '08

09 Jun '08

i can start phenix with new .pdb/.mtz, and custom geometry with satisfactory output. problem is, when i provide that output .def file (possibly w/ custom geometry in it) on the command line, phenix always sets up disulfides when it didn't before: Number of disulfides: simple=4, symmetry=0 Simple disulfide: " SG CYS A 14 " - " SG CYS A 14 " distance=0.10 Simple disulfide: " SG CYS A 140 " - " SG CYS A 140 " distance=0.08 Simple disulfide: " SG CYS A 144 " - " SG CYS A 144 " distance=0.54 Simple disulfide: " SG CYS A 147 " - " SG CYS A 147 " distance=0.18 Custom bonds: Sorry: More than one atom selected: "chain A and resname CYS and resid 140 and name SG" Number of selected atoms: 2 my ligands are attached to the cysteines, so i suspect some trouble here but can't see it - shouldn't be a problem, right? if i set disulfide_distance_cutoff= 1.0 or less, phenix drives the system into swap. any pointers, appreciated. -bryan

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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 22 May '08

22 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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