September 2012 - phenixbb - phenix-online.org

Scaling for Isomorphous Difference Maps
by Michael Thompson 20 Sep '12

20 Sep '12

Hello All, I'm currently using the GUI to calculate some Fo-Fo isomorphous difference maps. From looking at the Phenix documentation, it hasn't become apparent to me if the tool that performs this calculation automatically scales the two sets of amplitudes to one another, or if the input mtz files need to be scaled together elsewhere before running the map utility. Any info 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

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Two versions of TFZ, molecular replacement
by 赵岩 19 Sep '12

19 Sep '12

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! --

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advice for speeding up cif_as_mtz
by Eric Williams 19 Sep '12

19 Sep '12

I'm currently running cif_as_mtz and model_vs_data on the whole PDB as part of my dissertation. Time has become a critical concern, and cif_as_mtz (dev-1141) is running very, very slowly (1-4 minutes per entry). Here's how I'm calling it: phenix.cif_as_mtz <sf_cif_fn> --ignore-bad-sigmas --merge --remove-systematic-absences --map-to-asu --symmetry=<pdb_model_fn> --output-file-name=<sf_mtz_fn> I'm hoping that perhaps someone could help me determine which command line argument(s) could be removed to provide maximum speed-up. Thanks. :) Eric

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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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