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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 03 Sep '11

03 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 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

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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] 28 Aug '11

28 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 26 Aug '11

26 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 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

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