- phenixbb - phenix-online.org

B-iso vs. B-aniso
by Yuri 18 Sep '12

18 Sep '12

Dear community, The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to properly refine it anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space-group it is equivalent to about a 1.24 A complete data set. However, I have had a couple of cases where anisotropic B-factor refinement significantly improved R-work and R-free, while maintaining a reasonable R-gap, for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors? Any thoughts/opinions/call-outs from the community are welcome. Cheers, -- Yuri Pompeu

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Monitoring MR_ROSETTA progress on a cluster
by Dmitry Rodionov 17 Sep '12

17 Sep '12

Hi Tom, How are you doing? Sorry to bother you again. I got my hands on a login to local cluster (MOAB) and started MR_rosetta there as well. Problem is, I have hard time figuring out what it is doing at this moment and if everything is under control. All I see in the queue are the original submission and a process it spawned less then a minute later. While a day ago there were 30 processes (that's how much I can have). All mr_rosetta.log files end with a list of methods to be run. MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/LIST_OF_JOBS_RUNNING says: /sb/home/drodionov/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1 /sb/home/drodionov/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log MISSING FINAL COUNT: 0 But the file happily exists : GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log .... Starting job 1000...Log will be: /sb/home/drodionov/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1000.log And that job successfully finished a while ago. Is everything ok with the run? Am I just being impatient? Thanks! Best regards, Dmitry

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Custom restraints editor
by Kristof Van Hecke 17 Sep '12

17 Sep '12

Dear, When I try to define additional 'planarity' restraints via the 'Custom restraints editor', I get the following error (see below): (I'm using the Phenix nightly build dev-1148 on a Mac Book Pro, OS X 10.5.8, but had the same problem with the official release version 1.8) I also tried to add these additional restraints to my restraints .cif file, but then rmsd values increase to unreasonably high values. (I just want to keep 2 chlorine atoms on a phenyl ring better in the same plane) Any ideas please..? Thank you very much Kristof Van Hecke --------------------- untimeError : Syntax error: missing closing quote (python_object, line 1) Traceback (most recent call last): File "/Applications/phenix-dev-1148/phenix/wxGUI2/Programs/Refine/ Dialogs.py", line 296, in OnUpdate new_phil = self.GetPhilObject() File "/Applications/phenix-dev-1148/cctbx_project/wxtbx/ custom_restraints.py", line 646, in GetPhilObject new_phil = self._index.master_phil.format(python_object=self._params) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1714, in format result.append(object.format(sub_python_object)) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1714, in format result.append(object.format(sub_python_object)) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1714, in format result.append(object.format(sub_python_object)) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1727, in format result.append(object.format(sub_python_object_i)) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1727, in format result.append(object.format(sub_python_object_i)) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 1094, in format words = type_as_words(python_object=python_object, master=self) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 151, in as_words source_info="python_object") File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ __init__.py", line 60, in tokenize_value_literal tokenizer.settings(contiguous_word_characters="")])) File "/Applications/phenix-dev-1148/cctbx_project/libtbx/phil/ tokenizer.py", line 249, in next where_str(O.source_info, char_iter.line_number))) RuntimeError: Syntax error: missing closing quote (python_object, line 1) Platform info: __FILE__ = /net/patchnose/scratch1/phenix/phenix-dev-1148/ cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Sep 3 2012 __TIME__ = 06:05:56 __i386__ __APPLE_CC__ = 5367 __GNUC__ = 4 __GNUC_MINOR__ = 0 __GNUC_PATCHLEVEL__ = 1 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __VERSION__ = 4.0.1 (Apple Computer, Inc. build 5367) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_51 PY_VERSION = 2.7.3 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG boost/TAG: 79991 os.name: posix sys.platform: darwin sys.byteorder: little platform.platform(): Darwin-9.8.0-i386-32bit platform.architecture(): ('32bit', '') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 2 Memory total: 4,294,967,296 Memory free: unknown import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = √Ö

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Sa_Omit_map_DNA_low_resolution
by Mikalai Lapkouski 15 Sep '12

15 Sep '12

Hello, I want to generate a simulated annealing omit map around DNA molecule in my protein-DNA complex for publication. My resolution is very low - 5A. 1. I deleted the whole DNA (947 atoms of DNA against 7543 for protein part) from pdb and ran phenix.refine with simulated_annealing=True. But resulted Fo-Fc in the omitted region is very weak. Is it because of the low resolution and because big part of the model was omitted? 2. Next, I wanted to generate a composit_sa_omit map as in this case DNA would be deleted in small portions and the resulted map would give me a map I can use for publication: phenix.autobuild data=inp.mtz model=whole.pdb (contains DNA) maps_only=True (to skip rebuilding) composite_omit_type=sa_omit omit_selection=DNA.pdb (contains only DNA coordinates). But the job runs too long and still it seems like it is doing rebuilding. Is this a correct command and correct action to create a sa_omit map for the DNA in my complex? Thank you a lot for the help, Nick

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Re: [phenixbb] Two versions of TFZ, molecular replacement
by yzhao 14 Sep '12

14 Sep '12

Hi, Some information may be needed. The model used to do molecular replacement is not an original homolog PDB file. I feed the homolog structure and sequence alignment to MR_rosetta, and I obtained an overall_best.pdb from AutoBuild(diffraction resolution is about 3. 5A). So I use this overall_best.pdb to run Phaser, and achieved a solution as I just mentioned. the overall_best.pdb from AutoBuild has no obvious regular secondary structure relative to the homolog structure, but their overall appearances are very similar. Before I run Phaser, I also checked native Patterson, there is no large off- origin peak. Additionally, the self rotation function and matthews_coef indicate there is a monomer in ASU. Thanks a lot! -- Yan Zhao Randy Read 写:Hi, There's an explanation of the TFZ== entry and how to interpret the job history on our web page:http://www.phaser.cimr.cam.ac.uk/index.php/ Molecular_Replacement#Has_Phaser_Solved_It.3F Basically, the TFZ=13.9 means that, in the translation search using the orientation that came from the rotation function, the Z-score of this peak was 13.9. However, we found that the TFZ was too sensitive to random errors in the orientation, so Phaser now computes what the TFZ score would have been if the orientation in the translation search had been the optimised one from the rigid- body refinement. (We call this the TFZ-equivalent, denoted as TFZ==.) So after the refinement (giving LLG=235), a random sampling of translations shows that the TFZ score would have been 5.0 for the refined orientation. The next two entries are the LLG after the final refinement at full resolution (239) and the TFZ score for that refined solution (again 5.0). What you see is very unusual behaviour. The TFZ -equivalent is almost always higher than the original TFZ, and I can't recall a case where it was significantly lower. One possible explanation occurs to me. If your crystal has translational NCS ( indicated by a large off-origin peak in the native Patterson) and you're searching for a dimer, a translation search with the dimer axis parallel to a crystallographic 2-fold would give a very sudden increase in the LLG when the dimer is in the right place relative to the crystallographic 2-fold to generate a model that obeys the translational NCS. Then, if the refinement changed the orientation of the dimer so that its axis was less parallel to the crystallographic 2-fold, that would reduce the modulation of the calculated data and reduce the TFZ. If these are the circumstances of your job, then you should be able to fix it by making sure that you have a recent version of Phenix, then running a job looking for 2 copies of the monomer. In that case, Phaser will take proper account of the translational NCS and there won't be any strange artefacts. If those aren't the circumstances, then I'm very puzzled and would appreciate receiving the data, model and other information needed to reproduce your job ( off-line) to check out what is going on! Best wishes, Randy Read On 14 Sep 2012, at 20:13, 赵岩 wrote:Hi everyone, I am trying to solve a structure though molecular replacement and I have obtained a suspected solution. The header of the solution as follows, REMARK TITLE [no title set] REMARK Log-Likelihood Gain: 238.884 REMARK RFZ=10.9 TFZ=13.9 PAK=2 LLG=235 TFZ==5.0 LLG=239 TFZ==5.0 REMARK ENSEMBLE 1 EULER 15.53 0.10 344.54 FRAC -0.499 -1.000 -0.499 At first sight, the solution has no problem(TFZ>8), but the second and third TFZ are very low. For a correct solution, the later TFZs always higher than the first TFZ. So I don't konw how to understand the later TFZs and what extent I can refer to them. Thanks a lot! -- _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb ------Randy J. ReadDepartment of Haematology, University of CambridgeCambridge Institute for Medical Research Tel: + 44 1223 336500Wellcome Trust/MRC Building Fax: + 44 1223 336827Hills Road E-mail: rjr27(a)cam.ac.ukCambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Anisotropic scale matrix in phenix.refine
by Alex Taylor 13 Sep '12

13 Sep '12

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Ligand geometry, Ideal vs. Observed
by Yuri 12 Sep '12

12 Sep '12

Hi everyone, I am trying to show that a ligand underwent catalysis during a soaking experiment. One of the things I would like to show is the geometry of the ligand, bond angles/lengths, dihedrals, etc... One of my models has a hi-res of 1.18A and the ligand density is really clear and complete. What is the best way to refine the ligand unrestrained and then generate measurements? Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)? ANy idea is welcome. Thanks a lot -- Yuri Pompeu

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Bond/Angle restraints for multiple copies of ligands/cofactors
by Eckhard Hofmann 12 Sep '12

12 Sep '12

Hi all, if the xray data reach real atomic resolution (say <1A), one can nicely refine cofactors w/o restraints. In intermediate cases, the existence of multiple copies allows to use the "SAME" option in SHELX refinement to restrain identical molecules to each other, somewhat like NCS, but on bonds and angles. Is there a possibility to do something similar with PHENIX? I have structures with up to 16 or more copies in the ASU (and several copies per chain), and 1.1A resolution. This would give me a very stable way to access unbiased information about stereochemistry. (Using NCS is of course not an powerful idea, as the torsion angles might vary between the different copies). Thanks for feedback, Eckhard -- Eckhard Hofmann <eckhard.hofmann(a)bph.ruhr-uni-bochum.de> Ruhr-Uni Bochum AG Proteinkristallographie, LS Biophysik, ND04/316 44780 Bochum Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762

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Advice on final refinement of twinned R3 structure: DETWIN and ML-target vs twin_lsq_sq target
by Bjørn Panyella Pedersen 10 Sep '12

10 Sep '12

Dear list I would like some advice on how to do the final refinement of a twinned structure: I have a 3.0A structure (sg R3) which is twinned. I have collected ~50 datasets and the estimated twin-fraction varies from 0.2 to 0.45 based on phenix.xtriage analysis (britton plot etc). The structure could only be solved by experimental phasing using _detwinned_ datasets (detwinned by the ccp4 program DETWIN). Refinement of the model was initially done using my highest resolution _detwinned_ dataset (3.0A, britton_alpha:0.21) and a ML target in phenix.refine. Lately I have switched to th twin_lsq_f target and refined using the 'unmodified'/twinned dataset. 1. I have tried systematically to detwin the dataset with different twin-fractions and then refine using the ML-target and my best refinements comes using an alpha of 0.2 (see attached figure). This fits the Britton plot etc. 2. xtriage estimated the twin-fraction to by ~0.21, but using twin_lsq_f, phenix.refine now gets alpha to be 0.31. This seems like a large increase to me? 3. Using the manually detwinned dataset and a ML-target gives better R-factors than using the twin_lsq_f target (see attached figure). Bottom line: How should I report/deposit this structure: A. Should I use the manually detwinned data and an ML-target to get a model that explains the data best (lowest R-factors). And deposit my structure with modified (i.e DETWINNED) structure factors. I fear that people would react strongly to the deposition of modified F_obs in the pdb. I could deposit both twinned and detwinned structure-factores but this might also confuse? OR B. Should I use the twin_lsq_f target and accept that my deposited model is not as good as I know it could be. And deposit my structure with the real (i.e TWINNED) structure factors. OR C. Something I'm not aware of means that refinement using the ML-target is not allowed on detwinned datasets, causing me to have artificially low R-factors. I hope I'm not missing something basic here.:) Thank for any advice, pointers and ideas! -Bjørn -- Bjørn Panyella Pedersen, PhD Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco MC2240, 600 - 16th Street S414 San Francisco, CA 94158-2517 Phone: +1 415-476-3937 E-mail: bjopp(a)msg.ucsf.edu http://www.msg.ucsf.edu

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error message on dev-1145 during den session
by fulvio saccoccia 07 Sep '12

07 Sep '12

Dear Phenix users, here you have an error occurred during a DEN refinement cycle on a twinned structure. Please, help me in order to overcome the problem. This is the command line I used to run phenix: phenix.den_refine data.mtz model.pdb twin_law=h,-k,-l output.prefix=DEN10 --overwrite main.ncs=true set_b_iso=50 convert_to_isotropic=true xray_data.high_resolution=3.6 nproc=4 secondary_structure_restraints=true optimize_xyz_weight=true optimize_adp_weight=true reference_model.file=3ZVJ-coot1.pdb use_geometry_restraints=true den.params fix_rotamers=true den.params is attached I was running phenix dev-1145 on a 64bit Debian machine. This is the error message: Running DEN torsion optimization on 4 processors... Running torsion simulated annealing ...trying gamma 0.0, weight 100.0 ...trying gamma 0.2, weight 100.0 ...trying gamma 0.0, weight 300.0 ...trying gamma 0.2, weight 300.0 Traceback (most recent call last): File "/usr/local/phenix-dev-1145/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/den_refine.py", line 21, in <module> den_refine.run(command_name="phenix.den_refine", args=sys.argv[1:]) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/den_refine.py", line 113, in run customized_master_params=master_phil) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/command_line.py", line 146, in run call_back_handler=call_back_handler) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/driver.py", line 1532, in run ncs_manager = self.ncs_manager) File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/strategies.py", line 830, in refinement_machine log=log) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line 88, in __init__ "serious error; please contact bugs(a)phenix-online.org.") % so) RuntimeError: DEN weight optimization failed: DEN cycle 1 rfree at start of SA cycle: 0.4642 k_rep = 1.00 tardy_tree summary: number of vertices: 16570 number of edges: 16855 find cluster loops: 0 repeats number of fixed vertex lists: 0 number of fixed vertices: 0 number of clusters: 7857 merge clusters with multiple connections: 1 pass number of hinge edges: 7857 number of loop edges: 0 number of loop edge bendings: 0 number of fixed hinges: 0 CAUGHT EXCEPTION: (argument #0) ARGUMENT LEADING TO EXCEPTION: (0.0, 100.0) Traceback (most recent call last): File "/usr/local/phenix-dev-1145/cctbx_project/libtbx/easy_mp.py", line 155, in __call__ result = O.func(arg) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line 227, in try_den_weight_torsion call_back_after_step=False) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py", line 228, in run reduced_geo_manager=reduced_geo_manager) File "/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py", line 86, in __init__ O.weights = target_weights.xyz_weights_result AttributeError: 'NoneType' object has no attribute 'xyz_weights_result' This is a serious error; please contact bugs(a)phenix-online.org. Thanks in advance Fulvio Saccoccia PhD student Dept. of Biochemical Sciences Sapienza University of Rome +390649910556

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