- phenixbb - phenix-online.org

Restraints for keeping base-pairs co-planar in RNA/DNA
by jens j birktoft 07 Sep '11

07 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 *

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MemoryError in phenix.refine
by Tanner, John J. 06 Sep '11

06 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

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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

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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 >

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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

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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

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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

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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

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Zinc-cysteine bond refinement in phenix_refine
by Zhang yu 01 Sep '11

01 Sep '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

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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

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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

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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

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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

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occ are not zerp
by Kenneth A. Satyshur 27 Aug '11

27 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

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Dealing with malformed ligand geometries in phenix.refine
by Francis E Reyes 27 Aug '11

27 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

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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

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unstable phenix?
by Kenneth A. Satyshur 26 Aug '11

26 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

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Weird Hydorgen refinement
by Yuri 24 Aug '11

24 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

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Reference model restraints in autobuild?
by Francis E Reyes 24 Aug '11

24 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

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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

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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

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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

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pdb conversion to 3.2 format
by Luca Pellegrini 23 Aug '11

23 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

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MR problem
by intekhab alam 22 Aug '11

22 Aug '11

Hi there I have a data of heterotrimer protein complex at 2.9A resolution. One protein consists of two domains. I tried phaser as well as molrep which gives a solution with only one domain. Rotation function and translation function were found to be fine for these solutions. I tried to find missing domain of the protein after fixing one of the domain or the other partner proteins using whole part or various truncations of missing domain. I also tried to find and build missing domain using Rosetta with the solutions of Molrep or Phaser as template. But, there were no solutions, or the solutions are clashed with other domain or proteins. Furthermore, R and Rfree is 30 and 40, respectively, and I could not reduce them further. There was almost no electron density map in the empty space so that I could not model manually. Plz guide me ,how can i look for the missing domain in the protein. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

2 1

matplotlib
by Ed Pozharski 21 Aug '11

21 Aug '11

This is really a rather esoteric issue, but I feel I need to mention this to save someone, depending on the situation, anywhere between five minutes of googling or two hours of hair-pulling. In a nutshell, phenix gui may in some circumstances screw up other programs that use matplotlib. I can't track down which specific phenix gui action causes it, but it's safe to assume that whenever matplotlib libs are used the subsequent calls to logarithmic scale plots (and likely other things) throw this error TypeError: coercing to Unicode: need string or buffer, dict found The solution is to erase the ~/.matplotlib/fontList.cache. The likely cause is that phinix gui calls on bundled matplotlib which is different from one I have installed (not to mention that I am using Lucid (because it's LTS) which has python 2.6 and not the 2.7 that is bundled with phenix). However, it still writes into the same ~/.matplotlib folder, thus I end up with incompatible data. Certainly, the problem will be gone when matplotlib gets bumped up to 1.0.1 in next Ubuntu release. This is yet another example of why the standalone installation approach is ideologically objectionable on modern Linux. But of course, the practical advantage gained by not having to package the software for any possible OS flavor/version users may choose outweighs the lower risks of package incompatibility and the reduced size of the packaged product. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs

5 5

formyl-methionine
by Yuri 20 Aug '11

20 Aug '11

Hello Everyone, Stupid question. I see density at my N-terminus that really looks like formyl-Met. I want to model it and refine. I notice REEl has FME ligand for the formyl-methionine, but I dont want to treat it as a "ligand" since it is covalently attached to SER 2. What is the best way to modify the MET residue? Cheers -- Yuri Pompeu

3 3

Definition of "Saenger Class"
by jens j birktoft 20 Aug '11

20 Aug '11

Hi All, Could somebody direct me to "saenger class" definitions used in base-pair restraints for DNA/RNA. Cheers Jens *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft e-mail: birktoft(a)nyu.edu <jens.knold(a)gmail.com> New York University, Dept. Chemistry Phone: 212-749-5057 *

2 1

phenix.phaser multiple pdbs
by G Y 17 Aug '11

17 Aug '11

Dear all, I am writing a bash script for running phenix.phaser automatically on an ensemble of multiple pdbs. These pdbs have been superimposed by other tools before running phaser. The following is what I wrote for the ensemble part in params.eff file: ensemble { model_id = a1 coordinates { pdb = model1.pdb pdb = model2.pdb pdb = model3.pdb pdb = model4.pdb rmsd = None identity = 0.9 } It runs well. When it finished, I want to confirm that it really run MR on all four models or on a ensemble of these models. However in .log file, I found at the refinement part it shown me: ---------- REFINEMENT ---------- There is 1 solution to refine Refining solutions 0% 100% |==| DONE Configuring ensembles --------------------- PDB file # 1: model1.pdb This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 **************************** Does this mean that phenix.phaser only run MR with the first model? Does it due to the way I wrote in my params.eff file? What would be the correct way? Many thanks! best, G

3 5

changing project directory
by Jens Kaiser 17 Aug '11

17 Aug '11

Hi all, I have project data on external hard drives. As I use several different file systems, and mount the drives in random order, I cannot rely on the device being mounted in the same mount point. In order to keep paths consistent, I link the project directories into my home. This used to work fine. I recently created a project, and phenix seemed to have used the real path instead of the link-path (That's not the problem, yet). I tried to manually edit ~/.phenix/project_db.phil, but it still tries to write in a non-existing directory. A naive 'grep -R "disk-1" ~/.phenix' did not reveal any obvious file either. Where can I change the directory associated with a project {per,con}sistently? Thanks for your time, Jens

2 1

nucleic acid secondary restraints breaking in 1.7.1-743
by Francis E Reyes 17 Aug '11

17 Aug '11

Hi all Traceback (most recent call last): File "/usr/local/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 "/usr/local/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 67, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 112, in __init__ hbond_params=self.params.hydrogen_bonding) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/__init__.py", line 494, in create_hbond_proxies log=log) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/__init__.py", line 286, in hydrogen_bond_proxies_from_selections log=log) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/base_pairing.py", line 415, in create_hbond_proxies if distance_values[i][2] != '_': IndexError: tuple index out of range When specifying a single base pair when using secondary_structure nucleic acids restraints Any ideas? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 6

modelling of disordered protein
by intekhab alam 16 Aug '11

16 Aug '11

Hi I solved an RNA polymerase structure in its native as well as in complex with chemical ligands (2.5A and C2 space group). The structure has been solved by MR a protein having 60% identity. The ASU has a monomer and dimer. Recently i complexed this RNA polymerase (protein A) with a highly flexible protein B and got the crystal. These crytsal also have C2 space group (resolution 2.3A) having similar cell parameters but has psudotranslation (17.34%). I tried MR using rosetta. HHpred server selected one of my deposited structure in PDB (3NAI 100% identity) as template. Rosetta MR gave 2 solutions one of which is dimer-monomer arrangement while the other one is a trimer. The values of these solution are below. Solution 1: trimer REMARK Log-Likelihood Gain: 10662.548 REMARK RFZ=16.5 TFZ=14.4 PAK=0 LLG=959 TFZ==23.2 RFZ=0.0 TFZ=48.9 PAK=0 LLG=3195 TFZ==55.6 (& TFZ==52.6) LLG+=(3191 & 7008) LLG=7024 TFZ==72.0 LLG=10663 TFZ==90.1 Solution 2: Monomer and dimer in ASU REMARK Log-Likelihood Gain: 2120.965 REMARK RFZ=39.7 TFZ=21.9 PAK=0 LLG=811 TFZ==37.7 LLG=2121 TFZ==43.6 REMARK ENSEMBLE ensemble_1 EULER 204.07 178.91 204.37 FRAC 0.499 Map and model fits well in both the cases with R and R free 26 and 30% respectively. My queries: 1. which one will be the correct solution? Is it possible that the protein B has resulted in the trimeric arrangement? 2. i cannot find any continuous 2Fo-Fc map for proteinB, but there are some continuous density at 0.7 which is very ambiguous. how can i improve the map so that i can model some fragments of my proteinB (protein B is of 73 amino acids and is predicted to be highly flexible and disordered. ((biochemical as well as bioinformatical analysis done )) I already have tried autobuild but it fails to build even a partial fragment of the proteinB. Kindly suggest how to proceed , or how can i prove the presence of protein B in the structure. Regards INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

2 1

LigandFit error
by Priit Eek 14 Aug '11

14 Aug '11

Hi, I'm getting this error when trying to run LigandFit from the GUI: The key gui_output_dir is not in var_type_dict…this means the command-line Wizard needs a conversion in the ligandfit.py script under 'Translating inputs' or else in excluded_inputs or else the Wizard SetVars routine needs this variable set Is this a bug? I am using the 64-bit dev-842 version on OS X 10.7 Lion. Best regards, Priit

2 1

Unexpected Occupancy refiniement for ligands...
by Yuri 14 Aug '11

14 Aug '11

Hey, So I am finishing up a model at 1.5 A and I tried to refine my ligands (3) and waters (468) in addition to altloc residues. The residues refine as expected e.g OccA + OccB = 1.0 and all atoms in A have OccA and all the atoms in B have OccB. My ligands on the other are being refined as the following: HETATM 6867 C1 MLA L 3 32.357 -28.612 7.978 0.93 23.77 C C HETATM 6868 O1A MLA L 3 31.209 -28.949 7.502 0.85 24.79 C O HETATM 6869 O1B MLA L 3 32.454 -28.160 9.141 0.70 22.70 C O HETATM 6870 C2 MLA L 3 33.553 -28.727 7.095 1.00 25.46 C C HETATM 6871 C3 MLA L 3 34.774 -28.070 7.627 0.92 28.45 C C HETATM 6872 O3A MLA L 3 34.830 -27.664 8.808 1.00 30.15 C O HETATM 6873 O3B MLA L 3 35.775 -27.948 6.840 1.00 30.23 C O HETATM 6874 HC21 MLA L 3 33.321 -28.281 6.139 1.00 30.56 C H HETATM 6875 HC22 MLA L 3 33.760 -29.776 6.943 1.00 30.56 C H Each atom is getting an individual occupancy assigned, which physically is impossible :) Any light? Could it be my selection syntax? Corrigendum: I think I sent a bug email last night about an error when writing mtz files in refinement. It was an accident. My naming convention was bad, thats why it crashed. Sorry -- Yuri Pompeu

3 4

R/Rfree discrepancy Phenix vs Refmac
by Sabine Schneider 12 Aug '11

12 Aug '11

Hello, I am refining a structure at 2.1A solved by MR. For curiosity I'm testing things like 'shaking' coordinates, simulated annealing, refinement Refmac vs Phenix and so on, to see what influence that has on stats, maps etc. For instance after MR I did a bit of shaking the coordinates with pdbset (noise 0.1), followed by simulated annealing in Phenix. Phenix states after SA: Start R-work = 0.2671, R-free = 0.2992 Final R-work = 0.2312, R-free = 0.2666 When I use the output pdb of phenix directly in Refmac (with same mtz as input for Phenix) Refmac tells me: Initial R factor 0.2392 R free 0.2887 So I am quite puzzled about the discrepancy. Or can someone tell me if I made an error in reasoning somewhere? Thanks a lot for the help! Sabine

6 8

getting the crystal form
by Bradley Hintze 12 Aug '11

12 Aug '11

I was wondering if there was a easy way to grab the crystal form for a given PDB code? -- Bradley J. Hintze Duke University Graduate Student Department of Biochemistry

2 1

phenix.grow_density documentation
by Joern Krausze 12 Aug '11

12 Aug '11

Dear all, could anybody please provide me with a documentation for phenix.grow_density? I did'nt find one on the Phenix homepage or elsewhere in the depths of the internet. Thanks in advance, 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 2

Large size display system
by jens j birktoft 12 Aug '11

12 Aug '11

Sorry if this topic is bit off-list We are looking for some advice regarding a presentation system that permit the display in high definition of interactive molecular graphic sessions (incl. PHENIX,COOT, PyMOL. CHIMERA etc ) to our research group (10-12 people). Ideally we would like a 32"-36" LCD monitor coupled to a computer equipped with the proper graphics card for the large display as well as 24" monitor . Any suggestions would be appreciated Cheers Jens *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft, Department of Chemistry, New York University e-mail: birktoft(a)nyu.edu <jens.knold(a)gmail.com> slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057* *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft e-mail: jens.knold(a)gmail.com slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057 *

3 2

Re: [phenixbb] rosetta fragment files -- corrected command
by Thomas C. Terwilliger 11 Aug '11

11 Aug '11

Hi again David, Sorry, corrected command below. Can you try the version of the script I put in phenix: phenix.adjust_robetta_resid fragments_in fragments_adjusted <start_resno> Let me know if that doesn't do it! All the best, Tom T >> Hi, >> >> I'm also trying to use rosetta with a protein that has more than 650 aminoacids. I have found the answer on last June to the similar question about the fragment files but I couldn't make the script to change the aminoacids numbers work so far >> http://www.phenix-online.org/pipermail/phenixbb/2011-June/017268.html >> >> However I think the script got out of format and I can't make it work. I have python installed however I'm a total beginner on python. >> >> Is it possible that I could have the scrip file so I don't lose the proper format? >> Also, should I replace something inside (like put the file name somewhere) so it works? >> >> Thanks in advance >> >> David Neves >> Institut de Biologie Structurale >> Grenoble France >> >>

1 0

rosetta fragment files
by David NEVES 11 Aug '11

11 Aug '11

Hi, I'm also trying to use rosetta with a protein that has more than 650 aminoacids. I have found the answer on last June to the similar question about the fragment files but I couldn't make the script to change the aminoacids numbers work so far http://www.phenix-online.org/pipermail/phenixbb/2011-June/017268.html However I think the script got out of format and I can't make it work. I have python installed however I'm a total beginner on python. Is it possible that I could have the scrip file so I don't lose the proper format? Also, should I replace something inside (like put the file name somewhere) so it works? Thanks in advance David Neves Institut de Biologie Structurale Grenoble France

2 1

autobuild mtz file
by intekhab alam 09 Aug '11

09 Aug '11

Hi there i run autobuild in phenix and have my model and mtz file. when i open my mtz file in coot using the option open mtz, a window pops " column label assignment" How can i convert this mtz file that can open in coot which has both 2fo-fc as well as fo-fc maps. -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

3 2

Intensity-Weighted Reciprocal Lattice
by Michael Thompson 06 Aug '11

06 Aug '11

Hello ccp4 & phenix BB members, I would like to view the intensity-weighted reciprocal lattice for several data sets that I have collected. (The data have been indexed, integrated and scaled with Denzo and Scalepack.) I was wondering if anyone could offer some advice on what might be the best and/or most practical way to do this? I know that there are several programs out there that can generate sections (i.e. 0,k,l) of the reciprocal lattice, such as LABELIT and xrayplot. Are there any other options for doing this, perhaps within ccp4 and/or phenix? I once saw someone give a presentation and they had a little video that showed a three dimensional section of the reciprocal lattice rocking back and forth, which was really cool. I liked this because I felt like it gave a much more holistic representation as opposed to viewing a bunch of individual sections. I don't know if there is an easy way to do this, or if this person somehow managed to create this 3D depiction from a series of sections. Any tips or recommendations would be appreciated. Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

3 4

adding hydrogens -> increasing clash score
by Tatyana Sysoeva 05 Aug '11

05 Aug '11

Hi! I have probably a very naive question - when one includes hydrogens into a refinement of a model build with data at ~3.6A clash score should not go up? I mean I am including hydrogens for a reason of improving the model quality when I cannot fit the sidechains into some density, etc. Can it be true that using default 3 macrocycles on a changed (reduced) model is not enough to minimize it? Thanks, Tanya

4 8

Alternate occupancies
by Yuri 05 Aug '11

05 Aug '11

Dear all, If tell phenix.refine to do occupancy refinement on resname HOH, will it still perform the default refinement for residues with alternate conformers? -- Yuri Pompeu

2 1

how to apply phi/psi helical restraints
by Daqi Tu 03 Aug '11

03 Aug '11

Hi, I was trying to restrain a relatively mobile region of my structure to be helical using Phenix secondary structure restraints. The result is very bad. It forces the N-O distance to be about 3A, but the phi/psi angles are all ugly. What is the way in Phenix I can apply phi/psi restraints just like in the old CNS, which had always worked nicely? Thank you. Daqi Tu

3 8

phenix.mr_rosetta
by Andreas Förster 03 Aug '11

03 Aug '11

Dear all, I've made the frightening plunge into the cold waters of Rosetta (3.3 this time) again, with an eye on using it with Phenix, and am sharing the joy. Things work, but: - Download rosetta_source and rosetta_database separately. The bundle doesn't contain all the files. - Compilation fails on RHEL 6.1 (gcc 4.5 issue) but sails on RHEL 5.5. - $PHENIX_ROSETTA_PATH must point to the Rosetta installation directory (where rosetta_source and rosetta_database sit). Don't be misled by the phenix.mr_rosetta documentation into setting $PHENIX_ROSETTTA_PATH (triple T). - all directories in the Rosetta installation must be made accessible to users find $PHENIX_ROSETTA_PATH -type d -exec chmod 755 '{}' \; Hope that helps someone. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

1 0

new optimize weight
by daqi tu 02 Aug '11

02 Aug '11

Hi, With Phenix dev-836, when optimize_xyz_weight and optimize_adp_weight are set to true, where can I find the optimal weights so I can directly put into the next run to save time (i.e. without optimizing any more). Previously it is a scale factor I can use for fix_wxc for example. But right now I can only see a weight factor. Thanks. Daqi

1 0

Re: [phenixbb] Third issue of Computation Crystallography Newsletter - Volume 2, Number 2
by Frank von Delft 01 Aug '11

01 Aug '11

Hi, just scanned through the article on automatic weight adjustment. If I had to summarise figures 1 and 2, I'd have to conclude that the latest weight optimization only occasionally produces better results than not doing it (fig 2); and that therefore the old optimization was considerably worse than doing nothing at all. Or have I misinterpreted it? Cheers phx On 28/07/2011 19:59, Nigel Moriarty wrote: > Dear Colleagues, > > I am pleased to announce the publication of the third issue of the > Computational Crystallography Newsletter: > > http://www.phenix-online.org/newsletter/ > > A listing of the articles and short communications is given below. > Please note that the newsletter accepts articles of a general nature > of interest to all crystallographers. Please send any articles to me > at > NWMoriarty(a)lbl.gov noting that there is a Word Template on the website > to streamline production. > > Articles > -------- > > Improved target weight optimization in phenix.refine > Mite-y lysozyme crystal and structure > > > Short communications > -------------------- > > A lightweight, versatile framework for visualizing reciprocal-space data > An extremely fast spotfinder for real-time beamline applications > Hints for running phenix.mr_rosetta > > > Cheers > Nigel >

2 3

Re: [phenixbb] problem in rosetta rebuilding
by intekhab alam 01 Aug '11

01 Aug '11

Hi, Tom sorry for the delayed response. I was abale to fix by running one model. rosetta is working fine now. thanks again Intekhab Alam On Thu, Jul 21, 2011 at 11:49 PM, Thomas C. Terwilliger < terwilliger(a)lanl.gov> wrote: > Hi Intekhab, > > I'm glad the test works at least. How about trying this: > > Run just the job that hangs, but instead of running 100 models...just run > one single model. Does that work? > > All the best, > Tom > > > >> Hi Tom > >> i tried the commnad line and it works well. we also have increased the > >> memory to 3GB (earlier it was 2GB) > >> but still the system hangs with no response overnight. > >> the specifications of my system is as: > >> Ubuntu 9.04 > >> GCC 4.2 > >> RAM 3GB > >> Rosetta 3.2 > >> Phenix 1.7.1 > >> the command line test using > >> "phenix_regression.wizards.test_command_line_rosetta_quick_tests > >> test_rosetta_rebuild" works well . > >> > >> regards > >> intekhab alam > >> On Tue, Jul 19, 2011 at 11:31 PM, Thomas C. Terwilliger < > >> terwilliger(a)lanl.gov> wrote: > >> > >>> Hi Intekhab, > >>> > >>> I'm not sure about the part about the machine shutting down...but here > >>> is > >>> a little test you can run to make sure that rosetta and phenix are > >>> working > >>> properly together in rebuilding a model: > >>> > >>> phenix_regression.wizards.test_command_line_rosetta_quick_tests > >>> test_rosetta_rebuild > >>> > >>> or a more complete set of tests: > >>> > >>> phenix_regression.wizards.test_command_line_rosetta_quick_tests > >>> > >>> All the best, > >>> Tom T > >>> > >>> > >>> > >>> >> On 07/19/2011 04:49 PM, intekhab alam wrote: > >>> >>> > >>> >>> Hi > >>> >>> i tried to run rosetta on a unix machine (ubuntu 9.04) for my data. > >>> Upto > >>> >>> MR step everything goes fine , but during the rebuilding step after > >>> 20 > >>> >>> cycles the computer shuts down. > >>> >> > >>> >> Interesting behavior for a Linux machine. > >>> >> > >>> >> Once the machine has rebooted, reading the output > >>> >> of the dmesg command and looking at events prior to the last boot > >>> >> may give you some information on why the computer hung. > >>> >> > >>> >> My guess is that you went out of memory while using mr_rosetta. > >>> >> > >>> >>> i have attached the log file for the autobuilding run of rosetta. i > >>> am > >>> >>> using phenix 1.7.1-743 version. > >>> >>> i will be grateful if some one helps me out > >>> >>> -- > >>> >>> INTEKHAB ALAM > >>> >>> LABORATORY OF STRUCTURAL BIOINFORMATICS > >>> >>> KOREA UNIVERSITY, SEOUL > >>> >>> > >>> >>> > >>> >>> > >>> >>> _______________________________________________ > >>> >>> phenixbb mailing list > >>> >>> phenixbb(a)phenix-online.org > >>> >>> http://phenix-online.org/mailman/listinfo/phenixbb > >>> >> > >>> >> _______________________________________________ > >>> >> phenixbb mailing list > >>> >> phenixbb(a)phenix-online.org > >>> >> http://phenix-online.org/mailman/listinfo/phenixbb > >>> >> > >>> > >>> _______________________________________________ > >>> phenixbb mailing list > >>> phenixbb(a)phenix-online.org > >>> http://phenix-online.org/mailman/listinfo/phenixbb > >>> > >> > >> > >> > >> -- > >> INTEKHAB ALAM > >> LABORATORY OF STRUCTURAL BIOINFORMATICS > >> KOREA UNIVERSITY, SEOUL > >> > > -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

1 0

I seem to be unable to select the map_coeff_labels for phenix.cut_out_density
by Pietro Roversi 01 Aug '11

01 Aug '11

Dear Tom I am trying to run phenix.cut_out_density but I seem to be unable to select the map_coeff_labels: viscount:~/sharpfiles/logfiles/Japanin-ID29-Phaser714.15> phenix.cut_out_density cycle_best_13.pdb eden_flat_55.0pc.mtz << EOF map_coeff_labels="FBshasol SIGFPsha PHIBshasol FOMshasol" EOF The output (see below) says I did not give SIGFP and it also picks the default F,PHI and FOM from columns 4,5,6 What am I doing wrong? Thanks! Pietro # cutout # # Cut out density from a map # Type phenix.doc for help Cutting out density Miller arrays in mtz_in: ['H', 'K', 'L', 'Fcentsha', 'PHIcentsha', 'FOMsha', 'HLA', 'HLB', 'HLC', 'HLD', 'FHsha', 'PHIHsha', 'FreeR_flag', 'FPsha', 'SIGFPsha', 'Fcentshasol', 'PHIcentshasol', 'FBshasol', 'PHIBshasol', 'PHIshasol', 'FOMshasol', 'HLAshasol', 'HLBshasol', 'HLCshasol', 'HLDshasol', 'FCshasol', 'PHICshasol'] Setting FP and PHI from map_coeffs Setting FP and PHI from map_coeffs Setting FP and PHI from map_coeffs Setting FP and PHI from map_coeffs Setting FP and PHI from map_coeffs Center of cutout region will be from model center at: [62.32560090909093, 43.68719545454543, 32.72059636363636] ------------------------ COPYRIGHT NOTICE --------------------------------- Los Alamos National Laboratory This program was prepared by Los Alamos National Security, LLC at Los Alamos National Laboratory (the University) under Contract No. W-7405-ENG-36 with the U.S. Department of Energy (DOE). The University has certain rights in the program pursuant to the contract and the program should not be copied or distributed outside your organization. All rights in the program are reserved by the DOE and the University. Neither the U.S. Government nor the University makes any warranty, express or implied, or assumes any liability or responsibility for the use of this software. ******************************************************* * --- RESOLVE --- * * * * Statistical density modification * * Automated model-building * * * * For on-line help * * see "http://solve.lanl.gov" * * * * This software uses library routines from the * * CCP4 suite (http://www.ccp4.ac.uk) for which * * the author is very thankful! * ******************************************************* (version 2.15 of 20-Mar-2010) (size = 6) Tom Terwilliger, Los Alamos National Laboratory, "terwilliger(a)LANL.gov" >pdb_in_memory Reading pdb_in from memory If "no_reuse_model" is not set then this model will also be used as starting point for model-building >no_build Model will not be built >mask_cycles 1 Number of mask/image cycles: 1 >minor_cycles 0 Number of minor cycles per mask/image cycle: 0 >no_build Model will not be built >cutout Cutting out density near cutout_center and writing to P1 cell >fine_grid FFT grid will be extra fine (1/5 of resolution) >no_sort The atoms in pdb_in will not be sorted. >resolution 1000 2.13352593412 Resolution range (A) is: 2.133526 to 1000.000 >cell1 15.0 15.0 15.0 90 90 90 Cell for cutout (cell1) is 15.00000 15.00000 15.00000 90.00000 90.00000 90.00000 >cutout_center 62.3256009091 43.6871954545 32.7205963636 Center of density for cutout (cutout_center) is 62.32560 43.68719 32.72060 >padding 5.0 Padding around cutout of density: 5 A >cutout_mask 1 Cutout mask type (1=box, 2=sphere, 3=mask around model): 1 >cutout_sphere 10.0 Radius of cutout of density around cutout_center: 10 A >rad_mask 5.0 Radius for creating solvent model: 5.000000 > All done with inputs Not writing any files as information returned in memory Building protein Setting up for building protein Standard fill-in residues: ALA A GLY G Standard main-chain atoms: N CA C O CB All main-chain atoms: N CA C O Max dist between adjacent N atoms: 6.000000 List of all residues: GLY ALA SER VAL ILE LEU MET CYS PHE TYR LYS ARG TRP HIS GLU ASP GLN ASN PRO THR List of 1-letter code of residues: GASVILMCFYKRWHEDQNPT List of number of atoms in side-chains: 0 1 2 3 4 4 4 2 7 8 5 7 10 6 5 4 5 4 3 3 checking license file.. solve2.access The date today is 31-jul-11. Your license is good until 15-dec-96. Space group name: Point group: Space group number : 96 Symmetry operators: 8 Done with lookup FP taken from column 4 No dataset found matching ID = 0 PHIB taken from column 5 FOM taken from column 6 Using HLA HLB HLC HLD coefficients WARNING: No SIGFP input data--output SIGFP column will be SIGFP=1.0 for all HKL! Reading in FreeR_flag Total of 5695 reflections read from file Guessing FreeR_flag corresponding to free reflections This can be set with free_id xx Free R reflections are those with FreeR_flag= 0 Total of 251 of 5695 reflections in test set High-resolution limit of input phased data: 3.21 Adding F000 term (0.0) to this list Closed mtz file Starting resolution: 3.20 max: 3.20 Space group is 96 Using symmetry operations from input MTZ file MATRICES: SYMMETRY ELEMENT 0 1 0 0 0 0 1 0 0 0 0 1 0 SYMMETRY ELEMENT 1 0 -1 0 0.5 1 0 0 0.5 0 0 1 0.75 SYMMETRY ELEMENT 2 0 1 0 0.5 -1 0 0 0.5 0 0 1 0.25 SYMMETRY ELEMENT 3 1 0 0 0.5 0 -1 0 0.5 0 0 -1 0.25 SYMMETRY ELEMENT 4 -1 0 0 0.5 0 1 0 0.5 0 0 -1 0.75 SYMMETRY ELEMENT 5 -1 0 0 0 0 -1 0 0 0 0 1 0.5 SYMMETRY ELEMENT 6 0 1 0 0 1 0 0 0 0 0 -1 0 SYMMETRY ELEMENT 7 0 -1 0 0 -1 0 0 0 0 0 -1 0.5 SPACE GROUP SYMBOL: P 43 21 2 CHECK ON SPACE GROUP SYMBOL: P 43 21 2 HALL SYMBOL : P 4nw 2abw Extra fine grids used for FFT Transformations from orthogonal to fractional and back: Orthogonal to fractional fractional x= 0.01183 X + -0.00000 Y + -0.00000 Z fractional y= 0.00000 X + 0.01183 Y + -0.00000 Z fractional z= 0.00000 X + 0.00000 Y + 0.01123 Z Fractional to orthogonal Orthogonal X= 84.50000 x + 0.00010 y + 0.00010 z Orthogonal Y= 0.00000 x + 84.50000 y + 0.00010 z Orthogonal Z= 0.00000 x + 0.00000 y + 89.05000 z Estimated # of atoms in au: 2510 Not separating out FREE set from other reflections for main cycles. Using all data. Results of wilson scaling: Scale on I = 3.274 B-value = 47.194 Scaling data with value of 3.274 Reading model density histograms from /software/xtal/PHENIX/phenix-1.7.1-743/solve_resolve/ext_ref_files/segments/rho.list Read total of 6 sets of density functions Highest value of ix, iy, iz in a.u: 143 143 18 nu nv nw: 144 144 144 Number of grid points in au: 373320 Mean fom of this map was: 0.84 Summary of starting FOM vs resolution RES FOM FOM-smoothed N 29.25 0.89 0.86 27 17.82 0.79 0.86 42 13.27 0.71 0.86 72 10.48 0.85 0.86 120 8.83 0.89 0.85 118 7.63 0.84 0.85 206 6.65 0.85 0.85 243 5.96 0.88 0.85 268 5.43 0.85 0.85 306 5.03 0.88 0.85 313 4.67 0.89 0.85 415 4.38 0.86 0.84 348 4.15 0.88 0.84 445 3.91 0.86 0.84 567 3.67 0.84 0.84 701 3.46 0.82 0.84 675 3.28 0.78 0.83 829 Mean fom of this map was: 0.84 Starting phases assumed to be experimental (To override, use "phases_from_resolve") Estimating optimal initial smoothing radius using the function: R=2.41 * (dmin**0.90) * (fom**-0.26) with dmin = 3.200273 and fom = 0.8443282 Leading to R= 7.174512 To override, set "wang_radius_cycle", "wang_radius", or "wang_radius_start" Setting final smoothing radius to 4.000000 To override, set "wang_radius_cycle", "wang_radius", or "wang_radius_finish" Using pdb_in from memory Center of molecule read in with 1081 atoms is 62.275337 43.672276 32.612022 Read 1081 atoms from PDB file for use in model-building MEMORY Solvent content will be 0.40 Using database entry 5 for histograms (" 3 A dehalogenase model ") Using all data for tests due to low number in test set (override with "use_free_for_test") Total mask cycles: 1 Total density modification mask cycles: 1 Cycle Ref NCS Use NCS Build image solvent Extend Cycles Test 1 NO NO NO NO YES NO 0 Mask cycle 1 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.40 Smoothing radius: 7.17 Using histogram-based mask Assuming this cycle is unbiased (no previous density modification) Plot 1 ------------------------------------------------------------------------------- Plot of probability that a grid point is part of protein region vs percentiles of grid points All points to the left of the "+" signs are in solvent masked region those to right are in protein masked region. The values of p(protein) should change from low to high approximately at the value of the fraction of solvent indicated by the "+" signs. The sharper the transition the better. Note: the mask is only used to make an estimate of the p(protein) The values of p(protein) are used to weight the contribution of each grid point to the probability of the map: p(rho) = p(rho|protein) p(protein) + p(rho|solvent) (1-p(protein)) This says that the probability that we would observe the value "rho" of electron density at this point is the probability that we would observe "rho" if this were really protein times the probability that this is protein, plus the probability that we would observe "rho" if it were really solvent, times the probability that it is solvent. Probability that grid points are in protein region 1.0 ...........................xxxxxxxxxxxxxxxxxxxxxxx . + xx . . + x . . + x . . + . . + x . . + . p(protein) . xxxxxx . 0.5 . xxxxxxxxxxxxx + . . + . . x + . . + . .x + . . + . . + . 0.0 ....................+............................. 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- Cutting region containing model out of map Box to be cut out of density (A) : 15 15 15 Box with padding (A) : 25 25 25 NX NY NZ for cutout box: 36 36 36 NX NY NZ with padding: 60 60 60 Center of cutout region (A): 62.3256 43.6872 32.7206 Using box for cutout mask Total grid points marked: 46656 not marked: 169344 Mean density in cutout region (no density offset applied ) 0.040 for 46656 points Number of points in padded region (set to 0.0): 169344 Output array in memory with 3600 reflections resolve exit_info: source_file: /net/longnose/scratch2/phenix/phenix-1.7.1-743/solve_resolve/resolve/cutout.cpp source_line: 252 status: 0 EndOfResolve Output map coeffs 3600 Writing output mtz: cutout.mtz Writing output pdb (offset to match output mtz): cutout.pdb Citations for cutout: Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D66:213-221. ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] On Behalf Of Thomas C. Terwilliger [terwilliger(a)lanl.gov] Sent: 05 July 2011 17:46 To: PHENIX user mailing list Subject: Re: [phenixbb] phenix.mr_rosetta: Inconsistent query numbering Hi Pietro, There is something that phenix.mr_model_preparation cannot read in Japanin.hhr (attached): phenix.mr_model_preparation Japanin.hhr gives the same error. I'll copy Gabor Bunkoczi and see if he can help with this. All the best, Tom T >> Dear all, >> >> my run of phenix.mr_rosetta stops with: >> >> ******************* ERROR ENDING *************** >> Inconsistent query numbering >> >> ******************* ERROR ENDING *************** >> >> I attach script and logfiles. >> >> Any suggestions? >> >> Thanks >> >> Pietro >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Phaser searching with density: how do I place my model on the solution?
by Pietro Roversi 31 Jul '11

31 Jul '11

Dear all, I succeded in finding a molecular replacement solution searching with the density I have in P43212 against a C2221 dataset, using the Phaser procedure documented in: http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model Question: what operators should I use for dmmulti now? Or put it another way, how do I put onto the C2221 placement my P43212 model? I tried using the Euler and xyz numbers fro0m the phaser sol file but they do not seem to produce a model that goes with the C2221 Phaser density. Any help is greatly appreciated Thanks Pietro

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