January 2012 - phenixbb - phenix-online.org

links in phenix summary
by Christian Roth 04 Apr '13

04 Apr '13

Dear all, thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions. I have summarised a few things which one might consider if nonstandard links are necessary. Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script: elbow.ligand_linking model.pdb Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary. Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement. For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using iotbx.show_distances your.pdb > all_distances Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix! Christian

3 2

How to include restraints when refining DNA?
by Xun Lu 03 May '12

03 May '12

Dear all, I am refining a protein-DNA complex structure at 2.9A resolution. The R/Rfree is 0.2181/0.2501, which is pretty good, but I can tell that the DNA is not well refined. Some sugar puckers are not right. The distances between some base-paired bases are kind of short (~2.5A). I've tried including a reference model for the DNA, or including a cif file, and I've also tried to turn on the secondary_structure_restraints.... nothing worked. I must have not done it in a correct way. But how to do it? And how to deal with sugar puckers? In refmac, I can set the distances between bases during the refinement, so there must be a way to do it in phenix as well? Any advice is welcome. Thanks! Xun -- Department of Molecular and Structural Biochemistry North Carolina State University

4 3

Problem with version 1.7.1-743 on OSX
by Miguel Ortiz Lombardía 06 Feb '12

06 Feb '12

Dear phenix developers, Last Friday (April 29) we upgraded phenix to its most recent version (1.7.1-743). Installation went smoothly on both Mac (10.6.7 64-bit) and Linux (Ubuntu 10.10 64-bit) machines. However, we observe that we cannot use phenix.refine (I don't know for the rest of the applications) from the GUI on the Macs. phenix.refine does work from the command line, though. So, whenever we try to add a pdb in the GUI, we get this error message: This application does not support the file type for /path/to/the/file.pdb (format: txt) If we try to open an mtz, it sometime works, but most often we get: PHENIX did not recognize the file type for /path/to/the/file.mtz! and on the terminal from where the GUI was started we can find: **SYMMETRY OPERATOR ERROR** Error in interpreting symop " X+2/3, Y+1/3, Z+1/3 " **SYMMETRY OPERATOR ERROR** Error in interpreting symop " -Y+2/3, X-Y+1/3, Z+1/3 " (and so on, so forth). Any clues ? Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

6 12

Picking Rfree in thin resolution shells using command line
by Simon Kolstoe 31 Jan '12

31 Jan '12

Dear phenixbb, I see from a quick google that it is possible to pick my Rfree's using thin resolution shells (coz I've got 20 fold NCS), however as I am someone who tries to avoid the GUI where at all possible, could someone let me know what the command line way of doing this is? Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Wolfson Drug Discovery Unit University College London Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------

9 14

labelit.index python error
by Christian Roth 31 Jan '12

31 Jan '12

Hi, I had a few images, some of them are very bad. So itried to index 1 of the pictures, and indexing went very well, but then a strange error appeared which I cannot relate to anything. What might be the problem here? Best Regards Christian labelit.index_dev-968 /hosts/vulcan1/mar345/moschuetz/064c2_4/064c2_4_001.mar2300 Beam center is not immediately clear; rigorously retesting 2 solutions Beam x 172.5 y 172.9, initial score 405; refined rmsd: 0.1445 <Z>=20.4 Beam x 171.8 y 175.6, initial score 335; refined rmsd: 0.2160 <Z>=14.9 LABELIT Indexing results: Beam center x 172.58mm, y 172.91mm, distance 209.93mm ; 80% mosaicity=0.25 deg. Solution Metric fit rmsd #spots crystal_system unit_cell volume :) 2 0.2528 dg 0.105 190 monoclinic mC 248.48 71.93 154.76 90.00 112.70 90.00 2551913 :) 1 0.0000 dg 0.076 203 triclinic aP 71.93 129.30 154.76 111.69 90.25 106.07 1275944 MOSFLM Integration results: Solution SpaceGroup Beam x y distance Resolution Mosaicity RMS :) 2 C2 172.89 172.41 209.92 2.54 0.250000 0.109 1 P1 172.88 172.36 209.85 2.37 0.250000 0.094 show_stack(1): /userdata-2/christian/phenix- dev-968/labelit/command_line/screen.py(84) top_level_indexing show_stack(2): /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/../../labelit/command_line/index.py(5) <module> libc backtrace (28 frames, most recent call last): /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8058241] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6) [0x4009fb56] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(main+0x17) [0x80582df] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(Py_Main+0xaba) [0x8058f2a] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyRun_SimpleFileExFlags+0xb5) [0x80f61fd] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyRun_FileExFlags+0xdc) [0x80f52cc] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyEval_EvalCode+0x22) [0x80d659e] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyEval_EvalCodeEx+0x603) [0x80d63f3] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyEval_EvalFrameEx+0x622e) [0x80d5ad6] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyEval_EvalFrameEx+0x3dc7) [0x80d366f] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyObject_Call+0x46) [0x806162a] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8147760] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/base/bin/python(PyEval_EvalCodeEx+0x4ba) [0x80d62aa] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8145ea2] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8064f09] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8089ab0] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8064f09] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8089ab0] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x807b94a] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x80a3710] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x8089ab0] /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python [0x80a3677] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/lib/libboost_python.so [0x4036b67b] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/lib/cbflib_ext.so(boost::python::objects::value_holder<iotbx::detectors::Mar345Adaptor>::~value_holder()+0x4a) [0x42a13f22] /lib/tls/i686/cmov/libc.so.6(fclose+0x1a0) [0x400e4640] /lib/tls/i686/cmov/libc.so.6(fclose+0x41) [0x4018f241] [0x4001d400] /userdata-2/christian/phenix-dev-968/build/intel- linux-2.6/lib/boost_python_meta_ext.so(boost_adaptbx_segmentation_fault_backtrace+0x1f) [0x4032231f] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319

2 1

There are still seats available for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 30 Jan '12

30 Jan '12

We are extending the deadline because seats are still available for RapiData 2012, the fourteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the tenth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 22 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

1 0

Rosetta-MR - How long does it take?
by Tri Ngo 27 Jan '12

27 Jan '12

Hi Phenix users, I tried to utilize the Rosetta-MR to solve an Esterase structure (389 residues, 2 molecules/asu) which has 22% sequence identity to the know structure. I used HHPred to prepare the alignment input and Robetta fragment server to generate the fragment files. I also performed a quick test of mr-rosetta by running the command phenix_regression.wizards.test_command_line_rosetta_quick_tests. I think there is no error on my input files or the system. However, the program never finished. It still shows me the "Placing Model..." status. It's running around 48 hours and still show the same log file (at "Running group of place_model" step). I am not sure if it's normal to wait days or weeks to get the work done when running Rosetta-MR? Thank you for your helpful input. Best wishes, Tri -- * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150 Cell: 010-7774-8210

2 1

Problems with opening Coot and Firefox from gui under RHEL 6.2
by Brick, Peter 26 Jan '12

26 Jan '12

Hi, I've installed Phenix 1.7.3-928 on a linux workstation by downloading the binary phenix-installer-1.7.3-928-intel-linux-2.6-x86_64-fc3.tar I'm running Red Hat Enterprise Linux Workstation release 6.2. (Mainly 64 bit libraries but some additional 32 bit libraries that are necessary to run Alwyn Jones' 32 bit version of O.) *Help and Firefox* When I click on the Help icon in the Phenix GUI I get the message: [pbrick@pb1 ~/test]$ phenix phenix_gui.htm Using browser /usr/bin/firefox phenix_gui.htm Using browser /usr/bin/firefox /usr/lib64/firefox-3.6/firefox: symbol lookup error: /usr/lib64/libgnome-2.so.0: undefined symbol: g_dgettext But if firefox is already running it opens a new tab and I receive no error message. Firefox is the version shipped with RHEL 6.2: firefox 3.6.24 (I notice that the mozilla website is offering version 9.0.1 for i686 processors.) *Starting Coot* When I click on the Coot icon in the Phenix gui no window opens but I can see the processes: coot, coot_build_phenix_coot.csh and coot-real running. In fact coot-real consumes 100% of the cpu of one of the cores. What I find really weird is if I look at the processes with the system monitor gui and right click and 'kill' coot-real then instead of killing the process the coot window opens. At the same time coot_build_phenix_coot.csh disappears and the cpu usage drops to zero. (Note: I've also tried the fc12 version. I found that the version of pymol distributed with phenix uses 32 bit libraries and I needed to install libXmu.so.6) Any suggestions as to what I might be doing wrong? Peter

5 6

a story of acetoacetate decarboxylase
by Kevin Jin 26 Jan '12

26 Jan '12

Dear all, I wrote a story for acetoacetate decarboxylase catalysis. I hope you will like it. http://www.jinkai.org/AAD_history.html http://www.jinkai.org/AAD_catalysis.html Regards, Kevin

1 0

Bond to symmetry mate
by Eike Schulz 26 Jan '12

26 Jan '12

Dear phenixbb, I am sure this is a trivial problem encountered before and that there is a solution to it however, I was unfortunately not able to solve it myself or with the help of the online documentation. The problem: In one of my structures a nucleic acid chain extends over several symmetry mates. How can I create and refine a bond (in my case 5'-phosphate to 3'-end ) to that symmetry mate? Many thanks in advance Eike

2 1