- phenixbb - phenix-online.org

FOM in output MTZ file from phenix.refine
by Joern Krausze 08 Sep '11

08 Sep '11

Dear all, there is no FOM comlumn in my output MTZ file from phenix.refine. According to the documentation, the MTZ with FOM should be written out by default. I did not find any option that would trigger FOM inclusion. What can I do to include FOM? Thanks, Joern ****************************************** Address: Joern Krausze Molecular Structural Biology Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany Email: joern.krausze(a)helmholtz-hzi.de Phone: +49 (0)531 6181 7023 (office) +49 (0)531 6181 7020 (lab) ****************************************** Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

2 1

Postdoc Position at LBNL
by Nicholas Sauter 07 Sep '11

07 Sep '11

Exploring New Horizons in Data Processing. The Computational Crystallography group at Lawrence Berkeley National Lab ( http://cci.lbl.gov) would like to recruit an outstanding postdoctoral scientist with a strong interest in the computational challenges at the forefront of structural biology. With synchrotron beamlines increasingly controlled automatically and remotely, and with CCDs being replaced by pixel-array detectors, software development is critical to future experimental success. Better algorithms are needed to realistically model the diffraction observed on the new detectors, and the blinding data acquisition speed will require a new focus on efficiency. Difficult challenges also remain for deriving structural information from free-electron laser experiments. Two years after first light at the LCLS, new research on data analysis has become increasingly vital. This position offers the opportunity to collaborate with Bay Area beamline developers at both the ALS and SSRL, and access to unprecedented data sets from LCLS nanocrystallography studies. Local resources include numerous groups developing crystallography methods, as well as expertise in computational hardware including graphics processing units. Software will be developed within an open-source paradigm, and is expected to have a worldwide influence on high-throughput structural biology. Candidates should have a recent Ph.D. in computational biology or a related field, as well as strong experience in instrumentation, software, or data analysis. Applications consisting of a statement of research interests, CV, list of publications, and three references should be submitted on the Web at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=73565 -- Nicholas K. Sauter, Ph. D. Computer Staff Scientist/Engineer Physical BioSciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713

1 0

Restraints for keeping base-pairs co-planar in RNA/DNA
by jens j birktoft 06 Sep '11

06 Sep '11

Hi everybody: What would be proper approach to generate restraints that will keep base pairs coplanar (or nearly coplanar) in RNA/DNA helical structures? Hydrogen bonds by themselves are not sufficient, at least not for low resolution refinement, <4Å Jens *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft e-mail: jens.knold(a)gmail.com slow-mail: Dept. Chemistry, NYU, 350 CPW , Suite 9F, New York, NY 10025 Phone: 212-749-5057 *

4 3

MemoryError in phenix.refine
by Tanner, John J. 05 Sep '11

05 Sep '11

I get the following error at the end of a phenix.refine run. The pdb file is produced, but the mtz file is empty. The resolution is 1.15 A and the cell is CRYST1 84.808 93.803 132.080 90.00 90.00 90.00 P 21 21 21 The version is PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.7.1 Release tag: 743 Platform: intel-linux-2.6 redhat-e5.6 I've seen this sort of thread on the bb previously. Is there a fix for this, other than using refmac? Thanks. Traceback (most recent call last): File "/linux/src/phenix-1.7.1-743/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/linux/src/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 107, in run map_manger.write_files() File "/linux/src/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 1430, in write_files map_coeff_dataset=self.write_mtz_file(), File "/linux/src/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 1419, in write_mtz_file params = self.map_params.map_coefficients) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/maps/__init__.py", line 512, in __init__ coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/maps/__init__.py", line 359, in map_coefficients_from_fmodel fill_mode = "dfmodel") File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line 1920, in electron_density_map fill_mode = fill_mode) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/map_tools.py", line 137, in __init__ self.fmodel = self.fmodel.fill_missing_f_obs(fill_mode = fill_mode) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line 1681, in fill_missing_f_obs fmodel=self, fill_mode=fill_mode) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/missing_reflections_handler .py", line 129, in fill_missing_f_obs fmodel = select_by_map_cc(fmodel = fmodel.deep_copy())) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/missing_reflections_handler .py", line 113, in select_by_map_cc update_f_mask = True) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line 723, in update_xray_structure force_update = force_update_f_mask) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/masks.py", line 268, in shell_f_masks self.compute_f_mask() File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/masks.py", line 321, in compute_f_mask fm_asu = asu_mask_obj.structure_factors(self.miller_array.indices(),i+1) MemoryError -- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tannerjj(a)missouri.edu http://www.chem.missouri.edu/TannerGroup/tanner.html

3 4

Error on Fedora 15
by Yuri 05 Sep '11

05 Sep '11

I tried the installer and the binary both give the same result. I notice every utility that is essentially a graphics utility (i.e. dataViewer3D, REEL, dataviewer2D) crashes. Any ideas? -- Yuri Pompeu

2 1

Sep 15, 2011 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 05 Sep '11

05 Sep '11

Dear Users, > > The deadline for Nov/Dec 2011 Collaborative > Crystallography proposals will be *Sep 15, 2011. * > > ---------------------------------------------------------------------------------------- > Through the Collaborative Crystallography Program (CC) at the > Advanced Light Source (ALS), scientists can send protein crystals > to Berkeley Center for Structural Biology (BCSB) staff researchers > for data collection and analysis. The CC Program can provide a > number of benefits to researchers: > > * Obtain high quality data and analysis through collaborating with > expert beamline > researchers; > * Rapid turn around on projects; and > * Reduced travel costs. > > To apply, please submit a proposal through the ALS General User > proposal review process for beamtime allocation. Proposals are > reviewed and ranked by the Proposal Study Panel, and beamtime is > allocated accordingly. BCSB staff schedule the CC projects on > Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only > non-proprietary projects will be accepted. As a condition of > participation, BCSB staff researchers who participate in data > collection and/or analysis must be appropriately acknowledged - > typically being included as authors on publications and in PDB > depositions. Please consult the website for additional information at: > > http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography > > ----------------------------------------------------------------------------------------- > How To Apply: > > To learn more, go to: > > http://www.als.lbl.gov/als/quickguide/becomealsuser.html > > To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll > down to "*Structural Biology beamlines (includes protein SAXS)*" > and click on "New Proposal." Enter your proposal information, with > attention to the following details: > > * For question 3/First choice, select "5.0.1 > (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." > * Check box (yes) in response to question (7) "Do you want collaborative > crystallography > (beamline 5.0.1 or 5.0.2 only) > * In question 4, please describe a specific research project with a clear > end point. > > In order to request CC time for Nov/Dec 2011 allocation period, > proposals must be submitted by *Sep 15, 2011.* > > The deadline for CC proposals for the time period Jan/Feb 2012 will be > Nov 15, 2011. > > Regards, > Banumathi Sankaran >

1 0

Error on Fedora 15
by Yuri 04 Sep '11

04 Sep '11

Hello everyone, I just installed fedora 15 on a machine and tried to get phenix running, Installation seems to have proceeded normally. When I tried opening REEL the program crashes and it gives me the following. error The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadDrawable (invalid Pixmap or Window parameter)'. (Details: serial 100331 error_code 9 request_code 137 minor_code 8) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) I know its a problem with my machine because this same version runs great on RHEL5 I also see some funny behavior with COOT...but thats another story Any help is greatly appreciated, I am not sure how to fix this situation. Best, -- Yuri Pompeu

2 1

phenix.refine is renaming experimental phase labels and the purpose of _refine_data.mtz?
by Francis E Reyes 04 Sep '11

04 Sep '11

Hi all When specifying exptl_fobs_phases_freeR_flags_1.mtz (HLAM,HLBM.HLCM,HLDM) as an experimental phase file in phenix.refine via the .def file, these HL coefficients are written to *_refine_data.mtz as HLA,HLB,HLC,HLD. Now forgive me if I'm incorrect but HLA,HLB,HLC,HLD != HLAM,HLBM,HLCM,HLDM ? (where the former should come from phaser_1.mtz and the latter from resolve_1.mtz reflecting the density modification step). Also it's not desirable to create a _refine_data.mtz as it's unclear where the experimental phase labels came from the first place. Suppose I'm doing iterative rounds of MRSAD (with updated models during model building), I may have several AutoSol directories containing MRSAD runs for updated models. How am I going to know where the HL's in *_refine_data.mtz came from? (grepping .def files?) It would be easier if the .def's contained the full paths of the original .mtz files and not a phenix combined data file. I may have my original reflections in one mtz, an R-free set in another, experimental phases in another, etc. F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

4 3

Problem with R-free assignment
by Jose Arcadio 02 Sep '11

02 Sep '11

Dear phenix.refine community: I am solving a protein structure using experimental phasing. In order to do that I combined two derivative isomorphous datasets into a double SAD experiment (to increase the individual weak anomalous power from each dataset) using SHARP.My resolution is 3.2 A, and the space group is C2221. I managed to build a model using the density-modified phases from SHARP. Then I started refining against one of my derivative datasets because my native dataset is non-isomorphous due to the heavy meal soaking.Then I made two mistakes :( 1. I did not realize at the beginning of my refinement-building rounds that I was refining against the dataset that showed the worst statistics. 2. I was using a dataset with only FP and SIGFP but not DANO and SIGDANO. I used the phases from my SHARP map (also the experimental phase restraints) Now I did a new run of refinement using my best dataset (better statistics) and also including the anomalous data FP, SIGFP, DANO and SIGDANO. Obviously, my R-work and R-free got pretty much better. Nevertheless, the R-free was better than R-work at the beginning of the run, at the end of the refinement R-free and R-work inverted as usually (being R-free worst than R-work) r_work = 0.2582 r_free = 0.2888 . Certainly, there was a mistake with a new assignment of the free set of reflections. Now I am aware that the set of free reflections has to be the same all over the refining procedure. Here are the questions How can I be sure that my R-free is still a safe cross validation of the correctness of my structure? Is it useful to perform a round of simulated annealing in order to erase any wrong information in my model and start the refinement rounds again? Do you have any suggestions? All the best Jose Farias

3 6

model minimzation?
by r n 02 Sep '11

02 Sep '11

Dear all, Is it possible to do force field energy minimization for protein/peptide using Phenix? I am interested in doing energy minimization for different side chain rotamers. Thanks ram

3 2

Zinc-cysteine bond refinement in phenix_refine
by Zhang yu 31 Aug '11

31 Aug '11

Dear all, I have been stuck in the problem for a while. I appreciate any suggestions. I have two zinc binding domain in my 3A structure which are Cys4 type. The geometry is OK for one domain, but it is not refined properly in the other one. The problems during phenix refinement are 1. Zinc is always refined to position ~0.5A off from its correct position 2. The refined bond lengths of four Cys-Zn are all below 2.3 3. Sometimes, distances between SG atoms of nearby cysteines are too close, and coot just connect them as disulfate bond. 4. Sometimes, I get the following message showing that all bond angles are outliers with >8 sigmas, I listed part of the outliers. Top angle outliers (sorted by deviation): atoms ideal model difference deviation (sigma) ---------------------------------------------------------------------------- SG CYS D1204 57.894 104.470 46.576 9.32 ZN ZN D2001 SG CYS D1112 SG CYS D1201 50.842 92.496 41.654 8.33 ZN ZN D2001 SG CYS D1204 SG CYS D1204 126.952 92.496 -34.455 -6.89 ZN ZN D2001 SG CYS D1201 SG CYS D1201 52.183 86.105 33.922 6.78 ZN ZN D2001 SG CYS D1112 SG CYS D1194 152.275 119.729 -32.546 -6.51 ZN ZN D2001 SG CYS D1112 SG CYS D1112 89.273 119.729 30.456 6.09 ZN ZN D2001 SG CYS D1194 I also post my metal.edit file for refinement refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_2 = name SG and chain D and resname CYS and resseq 1201 distance_ideal = 2.310000 sigma = 0.100 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_2 = name SG and chain D and resname CYS and resseq 1194 distance_ideal = 2.310000 sigma = 0.100 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_2 = name SG and chain D and resname CYS and resseq 1112 distance_ideal = 2.310000 sigma = 0.100 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_2 = name SG and chain D and resname CYS and resseq 1204 distance_ideal = 2.310000 sigma = 0.100 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1194 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1201 angle_ideal = 112.172178 sigma = 5 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1112 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1201 angle_ideal = 87.092184 sigma = 5 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1112 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1194 angle_ideal = 118.116518 sigma = 5 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1204 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1201 angle_ideal = 91.677138 sigma = 5 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1204 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1194 angle_ideal = 130.829256 sigma = 5 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1204 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1112 angle_ideal = 104.886672 sigma = 5 } } Questions, 1. Why the ideal bond angle are different in the metal.edit file and final model ? How does phenix determine the ideal bond_angle? For example, in the metal.edit file atom_selection_1 = name SG and chain D and resname CYS and resseq 1204 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1112 The angle_ideal = 104.886672 But in the final model atoms ideal model difference deviation (sigma) ---------------------------------------------------------------------------- SG CYS D1204 57.894 104.470 46.576 9.32 ZN ZN D2001 SG CYS D1112 2. Do I need to put the following LINK in the pdb header to run refinement? LINK ZN ZN D2001 SG CYS D1201 1555 1555 2.34 LINK ZN ZN D2001 SG CYS D1112 1555 1555 2.33 LINK ZN ZN D2001 SG CYS D1194 1555 1555 2.38 LINK ZN ZN D2001 SG CYS D1204 1555 1555 2.37 3. After phenix refinement, the output pdb doesn't contain these LINK lines no matter what the inpout pdb is. Does phenix_refine use these restrains of LINK lines? Thanks. Yu Zhang Postdoc fellow Rutgers University

3 2

phenix utility for cif->pdb?
by Francis E Reyes 29 Aug '11

29 Aug '11

I need to check a monomer library definition. Is there a phenix utility that'll make cif -> pdb easily? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 1

Parallelization for optimization of wxu/wxc?
by Schubert, Carsten [JRDUS] 29 Aug '11

29 Aug '11

Hi, I was wondering if the optimization of the xyz and adp target weight could be parallelized and take advantage of multi-cpu systems? On the project I am working on now, the refinement time increased ~5.4 fold when with active optimization of these weights. Are there any plans for that in the works? Cheers, Carsten

5 5

symmetry related bond restraint
by Bryan Lepore 28 Aug '11

28 Aug '11

[ dev-837 ] I am trying to understand a symmetry operation from coot as it bears on phenix bond in the geometry restraints. in essence: in coot, origin-pre-shift is (-1 0 0) and the symmetry-related atom I want is Y,X,-Z + (0 1 1) however, the correct operation in phenix is Y,X,-Z+1 ... I suspect I simply do not understand the transformation. if i could at least confirm this math is correct, i'd appreciate it. -Bryan supplemental: * SG92 * apparently correct because the geometry checks fail otherwise * the scenario is similar to the thread linked below: http://www.phenix-online.org/pipermail/phenixbb/2010-April/015000.html * essentially a crosspost by me on coot the other day : https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=COOT;e45be09a.1108 * coot 0.6.2 rev-3562

3 2

Recovering Autobuild from tty disconnect
by Francis E Reyes 27 Aug '11

27 Aug '11

Our job submission node disconnects 'idle' after 4 hours of inactivity. As most grid / autobuild jobs take about that long I end being disconnected while the grid jobs complete. [1] Screen is not an option since access to the job submission node is via a load balancer and none of the job submission nodes allow access unless you're coming from the load balancer . i.e. there's no way to get to original machine where your screen has been started [2] all processes are sent SIGKILL during this automatic logout preventing the use of nohup.. will background=True work? [3] In the meantime, is it possible to resurrect the current autobuild? I've got FINISHED in all the autobuild's submitted to the grid, but everytime I try to combine_only=True run=my_run_number, I start from the beginning (with submitting the autobuild jobs to the cluster) even when I've moved the best of each build into MULTIPLE_MODELS. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 1

occ are not zerp
by Kenneth A. Satyshur 26 Aug '11

26 Aug '11

I am running omit map on pdb file and I get Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_22_/edited_pdb.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting... /usr/keck/u1/PriA/APS_Aug2011/phasing/AutoBuild_run_22_/LAST.LOG may have additional information... All occupancies in input PDB file are zero. yet CRYST1 85.433 85.433 111.682 90.00 90.00 120.00 P 32 SCALE1 0.011705 0.006758 0.000000 0.00000 SCALE2 0.000000 0.013516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008954 0.00000 ATOM 931 N ALA N 308 4.340 -30.086 -9.129 1.00 39.02 N ATOM 932 CA ALA N 308 4.553 -29.451 -10.458 1.00 38.92 C ATOM 933 CB ALA N 308 3.225 -29.326 -11.198 1.00 38.66 C ATOM 934 C ALA N 308 5.202 -28.079 -10.295 1.00 37.85 C ATOM 935 O ALA N 308 5.278 -27.555 -9.185 1.00 38.80 O ATOM 936 N ALA N 309 5.633 -27.505 -11.414 1.00 36.99 N ATOM 937 CA ALA N 309 6.216 -26.142 -11.498 1.00 37.18 C ATOM 938 CB ALA N 309 5.194 -25.019 -11.222 1.00 36.42 C ATOM 939 C ALA N 309 7.457 -25.985 -10.646 1.00 34.05 C ATOM 940 O ALA N 309 7.404 -26.148 -9.436 1.00 31.65 O ATOM 941 N ALA N 310 8.570 -25.673 -11.311 1.00 34.03 N ATOM 942 CA ALA N 310 9.883 -25.614 -10.696 1.00 34.33 C ATOM 943 CB ALA N 310 10.332 -24.166 -10.573 1.00 31.89 C ATOM 944 C ALA N 310 9.895 -26.350 -9.337 1.00 36.59 C ATOM 945 O ALA N 310 10.250 -25.773 -8.304 1.00 40.46 O ATOM 946 N ALA N 311 9.479 -27.623 -9.364 1.00 36.20 N ATOM 947 CA ALA N 311 9.321 -28.471 -8.174 1.00 33.93 C ATOM 948 CB ALA N 311 8.446 -29.664 -8.503 1.00 34.46 C ATOM 949 C ALA N 311 10.659 -28.948 -7.641 1.00 32.37 C ATOM 950 O ALA N 311 10.943 -30.156 -7.619 1.00 31.59 O ATOM 951 N ALA N 312 11.479 -27.982 -7.229 1.00 30.93 N ATOM 952 CA ALA N 312 12.821 -28.234 -6.694 1.00 30.94 C ATOM 953 CB ALA N 312 12.740 -28.872 -5.308 1.00 30.60 C ATOM 954 C ALA N 312 13.680 -29.080 -7.647 1.00 30.22 C ATOM 955 O ALA N 312 13.405 -29.148 -8.853 1.00 32.14 O ATOM 956 N PRO N 313 14.739 -29.702 -7.116 1.00 28.06 N ATOM 957 CA PRO N 313 15.519 -30.706 -7.852 1.00 27.14 C ATOM 958 CB PRO N 313 16.820 -30.771 -7.044 1.00 27.81 C ATOM 959 CG PRO N 313 16.871 -29.482 -6.264 1.00 28.11 C they don't look zero to me. anyone get this error? -- Kenneth A. Satyshur, M.S.,Ph.D. Associate Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

2 1

Dealing with malformed ligand geometries in phenix.refine
by Francis E Reyes 26 Aug '11

26 Aug '11

Hi all I've got 3.0A data and I'm ending up with distorted ligand geometry in phenix.refine. The model is complete and fitting the ligand is the final step (refined with individual_sites and individual_sites_real_space as suggested by an earlier posting). I've tried with a wxc_scale of 0.001 and it still looks wonky (tetrahedral C's not being so, etc). My cif is coming from phenix's internal db. Any suggestions? F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

3 2

maybe not a phenix issue, but with mr_rosetta:
by Francis E Reyes 26 Aug '11

26 Aug '11

What exactly is the nature of the fragment files used for MR/rebuilding? I'm an RNA guy and may have to generate them myself for certain projects. F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 1

unstable phenix?
by Kenneth A. Satyshur 25 Aug '11

25 Aug '11

We are running phenix (743) on a RHEL5 dual quad, multithread, making a composite omit map pf a very large structure (750 AA) and the system keeps getting locked up. Have anyone else seen this type of problem? Does multiprocessing work well on RHEL or just FC versions? We needed to install the FC8 version (/phenix-1.7.1-743/build/intel-linux-2.6-x86_64) to get it to work. So maybe we are using the wrong version? Shoiuld I recompile it for our system? Why is the gui always open when we are running long jobs (many days)? We need to put this stuff in the background and log out so someone else can run. Should scripts be used instead of the gui? Great program but too unstable. kas -- Kenneth A. Satyshur, M.S.,Ph.D. Associate Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

4 4

Weird Hydorgen refinement
by Yuri 23 Aug '11

23 Aug '11

Hi guys, I DEFINETELY ran refinement after I removed the hydrogens. My Rfree went up from 0.159 to about 0.167. Thanks for the tips. Ill give pdb.tools a try... -- Yuri Pompeu

3 2

Reference model restraints in autobuild?
by Francis E Reyes 23 Aug '11

23 Aug '11

Hi all While it is possible to generate refinement parameters to pass into autobuild, how does one pass the reference structure into the autobuild jobs if one were to refine using geometry restraints from the reference structure? (command line autobuild) If I can't supply the reference pdb, is there a phenix cmd utility that'll spit out all the restraints given a pdb so I can supply them in the refinement parameters file? F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

1 1

Re: [phenixbb] Weird Hydorgen refinement
by Yuri 23 Aug '11

23 Aug '11

Hi Pavel, The pdb did have anisou records for H's. I believe that is because in some previous runs I had only selected chain 'A' - I left out "and not elemnt H" - which I believe caused the H's to get refined anisotropically. I am trying to get rid of the ANISOU records and Ill run refinement again. ps. I am getting ready to deposit the coordinates and I dont want to keep hydrogens in the model, how can I get rid of them? I ve been using pyMol to remove them, but pymol gets rid of all the info -including symmetry -that phenix adds... Thanks -- Yuri Pompeu

3 2

Weird Hydorgen refinement
by Yuri 23 Aug '11

23 Aug '11

Hello everyone. I was trying to refine my model anisotropically. I selected element NA or (chain A and not element H). I looked at the output pdb shows that hydrogens were being refined anisou as well as the protein. I believe its because technically they are also in chain A, but shouldnt the default be never refine H's anisotropically, especially at 1.5A ?. -- Yuri Pompeu

2 1

autosol error in GUI
by r n 23 Aug '11

23 Aug '11

Hi all I downloaded the Phenix developing version 842, autosol gui running gave me the following error, "The key gui_output_dir is not in var_type_dict....command line wizzard needs conversion in the autosol.py script uing translating inputs or else in excluded inputs....wizard setVars routine needs this variable set". I have not had this error earlier version. any help? Thanks ram

2 1

pdb conversion to 3.2 format
by Luca Pellegrini 22 Aug '11

22 Aug '11

Hi, I am trying to use iotbx.pdb_remediator to convert PDB atom names to 3.2 format (as suggested by Nat Echols in a recent post to Coot mail-list). Unfortunately I get the following error message: lp212-mp2281 58% iotbx.pdb_remediator file_name=refine.pdb output_file=refine_3.2.pdb_file Traceback (most recent call last): File "/usr/local/cctbx/cctbx_sources/iotbx/command_line/pdb_remediator.py", line 54, in <module> run(sys.argv[1:]) File "/usr/local/cctbx/cctbx_sources/iotbx/command_line/pdb_remediator.py", line 51, in run remediator.remediator(params) File "/usr/local/cctbx/cctbx_sources/iotbx/pdb/remediation/remediator.py", line 257, in remediator user_dict) File "/usr/local/cctbx/cctbx_sources/iotbx/pdb/remediation/remediator.py", line 95, in build_hash test=os.path.isfile), "rb") TypeError: coercing to Unicode: need string or buffer, NoneType found It looks like a python problem, but I am afraid my insight ends here. Can anyone tell me how to fix this, please? I am not sure if it matters, but iotbx_pdb_remediator was not in my phenix installation (PHENIX-1.7.1-743 on MacOSX 10.6.8), so I installed cctbx separately. Thanks! Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

2 1