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Re: [phenixbb] Lysozyme/Xenon derivatives & Phenix.
by Terwilliger, Thomas C 02 Feb '12

02 Feb '12

Hi Brennan, The number of sites that you ask for affects the HYSS heavy-atom search procedure, but not too much else. Once some sites are found by HYSS, then autosol uses phaser to identify additional sites (that's why you got 22 sites, not 2). I am a little surprised that changing the number of sites from 2 to 4 makes the difference between finding correct sites and not finding them at all, but it does seem possible. For your experiment, one thing you could do: once you figure out where the "standard" Xe sites are, just feed them in to autosol with a sites_file=xxx.pdb for all your datasets. Then they are all starting out with pretty much the same information. All the best, Tom T ________________________________________ From: CCP4 bulletin board [CCP4BB(a)JISCMAIL.AC.UK] on behalf of Brennan Bonnet [Brennan.Bonnet(a)LIGHTSOURCE.CA] Sent: Thursday, February 02, 2012 9:43 AM To: CCP4BB(a)JISCMAIL.AC.UK Subject: [ccp4bb] Lysozyme/Xenon derivatives & Phenix. Hi all, I have a strange result using Phenix's AutoSol to look for xenon sites in lysozyme. For a few months now I have been trying to produce xenon derivatives of lysozyme using pressures in the range of 50-350psi and time ranges between 5-60min trying to find the "sweet spot" so that this technique can be applied to other proteins. For each dataset, I AutoSol using phenix and have it look for 2, 3, and 4 xenon sites. I haven't had much success though and typical values when asked to look for 2 sites have been Rwork/Rfree = 0.5585/0.5892, CC=0.14, Bayes-CC=6.5 and with xenon sites: (a, b, c, alpha, beta, gamma, space group) CRYST1 78.870 78.870 36.940 90.00 90.00 90.00 P 41 21 2 (columns after numbering are a, b, c, occ, B factor) HETATM 1 XE XE Z 1 48.601 67.475 1.088 0.06 6.58 XE HETATM 2 XE XE Z 2 54.986 76.636 2.746 0.11 7.49 XE which, to me, says that there is no binding (or at least nothing obvious). I finally got a good result though with 350psi and 5 minutes pressurization. After AutoSol, FOM=0.436, Bayes-CC=33.57, Model CC=0.83, Rwork/Rfree=0.2843/0.3023, 117/125 residues build and placed. And even though I told it to only look for 2 sites, Phenix went ahead and found 22 sites: (a, b, c, alpha, beta, gamma, space group) CRYST1 79.130 79.130 36.920 90.00 90.00 90.00 P 43 21 2 (colums after numbering are a, b, c, occ, B factor) HETATM 1 XE XE Z 1 -36.117 -56.764 -1.825 0.18 9.43 XE HETATM 2 XE XE Z 2 -54.805 -54.805 0.000 0.14 6.44 XE HETATM 3 XE XE Z 3 -8.337 -31.695 -16.766 0.08 8.26 XE HETATM 4 XE XE Z 4 -5.702 -64.959 -35.134 0.05 5.21 XE HETATM 5 XE XE Z 5 -9.535 -22.397 -31.839 0.06 14.33 XE HETATM 6 XE XE Z 6 -7.319 -66.343 -35.123 0.05 6.02 XE HETATM 7 XE XE Z 7 -8.580 -21.153 -30.274 0.05 7.43 XE HETATM 8 XE XE Z 8 -1.494 -29.583 -2.339 0.06 7.36 XE HETATM 9 XE XE Z 9 -0.518 -16.483 -16.776 0.05 6.56 XE HETATM 10 XE XE Z 10 -0.464 -29.847 -4.386 0.06 6.04 XE HETATM 11 XE XE Z 11 -1.222 -16.234 -18.952 0.04 6.51 XE HETATM 12 XE XE Z 12 -6.001 -20.380 -4.532 0.05 7.22 XE HETATM 13 XE XE Z 13 -5.169 -27.522 -10.128 0.05 3.54 XE HETATM 14 XE XE Z 14 -11.931 -67.039 -4.699 0.05 7.96 XE HETATM 15 XE XE Z 15 -6.538 -10.408 -3.761 0.04 10.22 XE HETATM 16 XE XE Z 16 -0.458 -23.897 -31.221 0.05 6.85 XE HETATM 17 XE XE Z 17 -3.308 -65.181 -8.754 0.03 8.08 XE HETATM 18 XE XE Z 18 -11.080 -29.129 -2.144 0.04 5.61 XE HETATM 19 XE XE Z 19 -5.720 -73.029 -2.035 0.04 11.24 XE HETATM 20 XE XE Z 20 10.236 60.097 33.822 0.03 5.38 XE HETATM 21 XE XE Z 21 5.980 68.581 3.532 0.03 7.49 XE HETATM 22 XE XE Z 22 11.107 13.277 27.334 0.03 7.10 XE I'm pretty sure there aren't 22 sites for xenon to bind in lysozyme but it looks to me like the top 2 (maybe top 3) are actual sites which is great. The strange part is that when I use the same data and have Phenix look for 3 or 4 sites it then only finds 3 or 4 very low occupancy sites and the CC's/R's are again all very poor. Has anyone had this problem or does anyone know what's going on? This is the first success that I'm having with xenon derivatization and it seems to me that if Phenix can find 22 sites when asked to find 2 it should have no problem when asked to find 3 or 4. Thanks in advance, ~Brennan~

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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 ---------------------------------------------------------------

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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

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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) =========================================================================

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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

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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

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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

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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

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Twin_law in GUI Phenix Refinement
by Tri Ngo 25 Jan '12

25 Jan '12

Hi phenix users, I have two questions when using Phenix Refinement. 1. I'd like to run phenix refinement with twin data but I don't know how to define twin_law using GUI Phenix refinement module in Linux. 2. I used phenix refinement in Windows to refine a 2.3A structure. My problem is the Rfree is quite high. - I applied twin refinement + TLS + NCS and SA refinement (wxu_scale = 1) Start: r_work = 0.2149 r_free = 0.2833 bonds = 0.016 angles = 1.988 Final: r_work = 0.2029 r_free = 0.2735 bonds = 0.008 angles = 1.448 - Then I use auto-weight to optimize the Rfree. optimize_xyz_weight = True optimize_adp_weight = True wxc_scale = 0.5 wxu_scale = 1 Start: r_work = 0.2152 r_free = 0.2735 bonds = 0.008 angles = 1.322 Final: r_work = 0.2309 r_free = 0.2781 bonds = 0.003 angles = 0.848 I think the bond rmsd and angle rmsd were too small in this final refinement. Do you think it's normal or I need to try more? Thank you very much for your helpful input. Best wishes, -- * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150 Cell: 010-7774-8210

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model_vs_data
by Karolina Michalska 25 Jan '12

25 Jan '12

Hi everybody, I 've run model_vs_data for one of my structures and here is what I got: Information extracted from PDB file header: program_name : REFMAC year : None r_work : 0.15793 r_free : 0.19845 high_resolution : 1.45 low_resolution : 36.92 sigma_cutoff : None matthews_coeff : None solvent_cont : None TLS : False (number of groups: 0) After applying resolution and sigma cutoffs: n_refl_cutoff : 26357 r_work_cutoff : 0.1450 r_free_cutoff : 0.1687 Can someone, please, explain why there is such a big difference in R values? When I do refinement in phenix I get practically the same results that Refmac produces. Thanks, Karolina

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