- phenixbb - phenix-online.org

MAD from many crystal
by Theresa H 04 Feb '12

04 Feb '12

Hi everyone. Can I do 3 wavelength MAD phasing with AutoSol GUI with data from multiple crystals? Is there a reference/guide that I can use? Thank you. Theresa

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structure comparison
by Christian Roth 03 Feb '12

03 Feb '12

Hi all, I tried the structure comparison in phenix validation and loaded seveeral structures and a sequence file. I started and than this strange error appears Did I specified something wrong? Best Regards Christian AssertionError : Traceback: File "/userdata-2/christian/phenix- dev-968/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/userdata-2/christian/phenix- dev-968/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/userdata-2/christian/phenix- dev-968/phenix/phenix/automation/structure_comparison/__init__.py", line 1041, in __call__ analyses = run(args=list(self.args), log=sys.stdout) File "/userdata-2/christian/phenix- dev-968/phenix/phenix/automation/structure_comparison/__init__.py", line 1006, in run analyses = manager(params.structure_comparison, log=log) File "/userdata-2/christian/phenix- dev-968/phenix/phenix/automation/structure_comparison/__init__.py", line 196, in __init__ self.run() File "/userdata-2/christian/phenix- dev-968/phenix/phenix/automation/structure_comparison/__init__.py", line 250, in run self.process_alignment() File "/userdata-2/christian/phenix- dev-968/phenix/phenix/automation/structure_comparison/__init__.py", line 370, in process_alignment log=self.log) File "/userdata-2/christian/phenix-dev-968/cctbx_project/mmtbx/msa.py", line 262, in align_pdb_hierarchies assert (reference_hierarchy is None)

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Re: [phenixbb] [ccp4bb] Lysozyme/Xenon derivatives & Phenix.
by Randy Read 03 Feb '12

03 Feb '12

Hi, I'm cross-posting this to the Phenix-BB, because you did this calculation in Phenix, but since the site completion for SAD phasing would be done with Phaser, the answer is relevant to both packages. Basically, I think Jim Pflugrath's suggestion is correct. Comparing your Xe coordinates to S and Cl coordinates from one of our test SAD phasing datasets, the majority of your extra sites are in the positions of either intrinsic S anomalous scatterers or bound halides. The Phaser completion step found them, even though you only asked for 2 sites initially, because it continues adding new sites as long as there are significant peaks in the SAD LLG maps. The refined occupancies make sense, assuming you were collecting your data around 1A wavelength. At that wavelength f" is about 4-5e for Xe and about 0.25-0.3 for S or Cl, and multiplying (say) 4.5e by occupancies of 0.03-0.08 gives effective f" values of 0.14-0.36e. Of course, Phaser isn't just trying to fit the imaginary part of the scattering, so the occupancies could end up slightly higher because it's trying to account for atoms with 16-17 electrons using partially-occupied atoms with 54 electrons. Knowing that, once Phaser has found the Xe atoms, it will then find the weak anomalous scattering from S and Cl, you could tell Phaser to look in addition for S atoms. (At around 1A wavelength, there's not enough difference between S and Cl, in either their real or anomalous scattering, to matter, so you don't need to look for Cl in addition.) Phaser will reassign atom types based on refined occupancy, so it would likely get most of these right, which would very slightly improve your phasing model (because you would then have the right ratio of real to imaginary scattering). Another advantage to looking for both atom types is that, when you mix atoms with different ratios of real and imaginary scattering, Friedel's law is broken even for the substructure structure factors, which has two consequences. First, the likelihood score will probably be significantly better for the correct enantiomorph than the incorrect one; second, you're likely to end up with a slightly more complete substructure when working with the correct enantiomorph. Note that AutoSol also chose the correct enantiomorph after phasing, by looking at map quality indicators for the two hands. Regards, Randy Read On 2 Feb 2012, at 16:43, Brennan Bonnet wrote: > 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~ ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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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 27 Jan '12

27 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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links in phenix
by Christian Roth 25 Jan '12

25 Jan '12

Hi, I have a pdb with a sugar chain as ligand. I used phenix ready set to get the links according to the link remarks in the pdb. However when I look into the edits file. All links are defined as geometry restraints and despite it is alpha 1-4 all bond restraints differ slightly in their length. Within the pdb file the definitions for the links were set to alpha1-4. A Similar thing happend with a peptide link between 2 Aminoacids which have not a continously numbering because of a deletion, but it is a simple peptide bond. I modified the .link.edits file accordingly for the sugars like this ---------- refinement.geometry_restraints.edits { apply_cif_link { data_link = ALPHA1-4 atom_selection_1 = name O4 and chain B and resname GLC and resseq 1 atom_selection_2 = name C1 and chain B and resname GLC and resseq 2 } } ------------ And applied a trans link for the peptide bond I added the modified file as additional parameter file in the gui. However in the final .eff file I found just the old restraints from the previous run. In the final .eff file it is stated that the file with my updated links is loaded ------ gui { base_output_dir = "/homes/roth/structure/250/082_c2_5/refinement/phenix" tmp_dir = "/homes/roth/structure/250/082_c2_5/refinement/phenix/phenix/tmp" send_notification = False notify_email = "christian.roth(a)bbz.uni-leipzig.de" add_hydrogens = True skip_rsr = False phil_file = "/homes/roth/structure/250/082_c2_5/refinement/phenix/refmac20link.link.edits" ----- Somehow the old restraits are already in the .eff file and the new ones are ignored how I could I avoid this. Simply closing the GUI an reopening? A second question is a very non standard peptide link due to a SNN residue in the chain. Based on the link a geometry restrain is created througn phenix.link_edits There is a slight difference in the length between the N- terminal and the C-terminal peptide bond. Which is probably fine and the resoution is good enough (roughly 2 Ang.) that is looks fine, but no angle definitions for phi psi and so on are stated. What is the best way to define this two bonds correctly for the subsequent refinement? A third question is a alpha1-4 link which extend to a symmetry related sugar. How I incorporate the symmetry information into the link? A last question regarding the hydrogens in refinement. For rebuilding it is nice to remove the hydrogens. Normally I use the commandline for this purpose. But It would be nice to do it automatically after refinement as a third pdb output in addition to the two standard outputs phenix_output.pdb and the phenix_output_reduce.pdb. Is there an option in the GUI to do this automatically. I thought I have seen this previously but cannot find it anymore I am sorry for this long Mail and so many question. I hope you could help me to clarify some the things. Best Regards Christian

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DEN Refinement in phenix 1.7.3
by Eike Schulz 24 Jan '12

24 Jan '12

Dear phenixbb, I have noticed that in (since?) the latest release it is possible to activate DEN refinement in phenix.refine. I assume this refers to deformable elastic networks right? What is your experience with DEN refinements ? As I could not find any reference to it in the documentation I would be happy to have feedback on when to use and when to avoid it e.g. resolution limits etc. and what to watch out for. Many thanks in advance Eike

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cif files
by Shya Biswas 24 Jan '12

24 Jan '12

Hi all, It appears that the cif file generated from prodrg (REFMAC format) is not recognised by phenix during refinement. Did anyone have similar issues or i am doing something wrong? somehow the geometries obtained from elbow are not right for my ligand so had to use prodrg to generate cif files. thanks, Shya

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Refinement of two co-factors/ligands at the same position
by Kornelius Zeth 23 Jan '12

23 Jan '12

Dear all, how can I refine two different co-factors/ligands ('XXX and YYY', with differing occupancy and cif-Files) located at the same position within an enzyme? What about the chain IDs, segment IDs etc? Thanks and best wishes Kornelius -- Kornelius Zeth ZMBP, Uni-Tuebingen Auf der Morgenstelle 1 72076 Tübingen Germany

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There's BARELY A WEEK left to apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 20 Jan '12

20 Jan '12

Half of the 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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phosphate stereochemistry
by Luca Pellegrini 20 Jan '12

20 Jan '12

Hi, I have noticed that Phenix mangles O-P bond lengths and angles in the phosphate groups of my DNA chain (example in pict attached). This only happens to 3 out of 28 phosphates. The refined protein-DNA structure does not present any other unusual stereochemistry issues and refinement runs normally. Could anybody advice on what is going on and how to fix this, please? I am using Phenix-1.7.3-928. Refinement is with default target weights, hydrogens on and does not include simulated annealing. I could make the stereochemistry targets more stringent, but the default values seem strict enough (bond and angle rmsd is 0.005 and 1.225). Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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phenix.refine is auto selecting an old .pdb file for refinement
by Andrews, Forest Hoyt 20 Jan '12

20 Jan '12

I'm having a bit of an issue with phenix.refine. I was receiving the following error "number of groups of duplicate atom labels: 4789 total number of affected atoms: 9578" However when I looked inside my .pdb file there where only 4789 atoms total....No duplicates. I discovered that phenix.refine is auto selecting a .pdb from a previous run. I found this out by not selecting any .pdb file and found phenix.refine refining my data with an older model I use to refine a previous round. How can I stop phenix.refine from auto selecting a .pdb during refinement? __________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Pavel Afonine [pafonine(a)lbl.gov] Sent: Friday, January 20, 2012 12:20 PM To: PHENIX user mailing list Subject: Re: [phenixbb] phosphate stereochemistry Hi Luca, what kind of NCS restraints did you use: torsion or Cartesian? I wonder if torsion NCS would naturally avoid this problem? I hope Jeff comments on this. Pavel On 1/14/12 10:51 AM, Luca Pellegrini wrote: > I think I discovered what was happening to my DNA molecule during > refinement, that caused distortion of the phosphate groups. It was > something along the lines of what Dale suggested, I mention it here so > that it might be useful to others. > > I have two DNA molecules in the ASU and I didn't realised that I had > accidentally swapped OP1 and OP2 in 3 out of 28 phosphates (so that, > if the two DNA molecules were superimposed, OP1 ended on top of OP2). > Because I had NCS restraints on during refinement, I guess phenix was > trying to move OP1 in one DNA molecule towards the NCS-equivalent > position of OP1 in the second molecule, hence the altered geometry. > > I have fixed the atom nomenclature problem and now the geometry of my > DNA is ok. I appreciate that most people tend to avoid such mistakes > ;-) but perhaps it would be good if phenix could flag situations such > as these. > > Luca > > On 6 Jan 2012, at 16:15, Pavel Afonine wrote: > >> Hi Luca, >> >> phenix.refine always generates a *.geo file that lists all the >> geometry restraints (bonds, angles, planarities, chiralities, >> dihedral, non-bonded, ncs(if any)) used in refinement for all atoms. >> For each restraint it list current model value, target (library) >> value, etc. >> >> Can you have a look at *.geo file for O-P bonds in question? May be >> this gives a hint about what's going on? >> >> Pavel >> >> On 1/6/12 4:31 AM, Luca Pellegrini wrote: >>> >>> Hi, >>> >>> I have noticed that Phenix mangles O-P bond lengths and angles in >>> the phosphate groups of my DNA chain (example in pict attached). >>> This only happens to 3 out of 28 phosphates. The refined protein-DNA >>> structure does not present any other unusual stereochemistry issues >>> and refinement runs normally. Could anybody advice on what is going >>> on and how to fix this, please? >>> >>> I am using Phenix-1.7.3-928. Refinement is with default target >>> weights, hydrogens on and does not include simulated annealing. I >>> could make the stereochemistry targets more stringent, but the >>> default values seem strict enough (bond and angle rmsd is 0.005 and >>> 1.225). >>> >>> Thanks, >>> Luca _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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Real_space_refinement at low resolution question
by fulvio saccoccia 20 Jan '12

20 Jan '12

Dear phenix users, I was wondering if it could be correct to exclude the real_space_refinement step working with a 3.3 A resolution map: I noted that in every real_space_refinemet step phenix told me that it was not useful. How can I exclude the routine from the command line? I am using 1.7.3-928 version.

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Real_space_refinement at low resolution question
by fulvio saccoccia 20 Jan '12

20 Jan '12

Dear phenix users, I was wondering if it could be correct to exclude the real_space_refinement step working with a 3.3 A resolution map: I noted that in every real_space_refinemet step phenix told me that it was not useful. How can I exclude the routine from the command line? I am using 1.7.3-928 version. Fulvio Saccoccia, PhD student Dept. of Biochemical Sciences Sapienza University of Rome

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problem converting PDB file to mmcif for deposition
by Salameh, Mohd A., Ph.D. 20 Jan '12

20 Jan '12

Hi Everybody, I encountered a problem recently in converting my PDB file to mmcif using the pdb_extract tool in rcsb. It simply writes out an empty file!! I wonder if any of you have faced such a problem before and know the solution!! I carefully examined the PDB file header and I couldn't really find a reason why this PDB failed to be converted. I only use PHENIX for molecular replacement and refinement. I used the default TLS refinement so I assume the whole structure will be refined as a group. I hope somebody is familiar with this can help me out. Thank you very much, Mohd

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real space correlation
by Jerome Nwachukwu 19 Jan '12

19 Jan '12

Hi: I am trying to run phenix.real_space_correlation from the command line and received the following error message. Is there a specific syntax i should use? Thank you, -Jerome Syntax error: expected "=", found "Date" (file "3_refine_001.pdb", line 1) Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/command_line/real_space_correlation.py", line 9, in <module> command_name = "phenix.real_space_correlation") File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/real_space_correlation.py", line 332, in cmd_run track_unused_definitions = True) File "/usr/local/phenix-1.7.1-743/cctbx_project/libtbx/phil/__init__.py", line 1718, in fetch assert source.name == self.name AttributeError: 'NoneType' object has no attribute 'name'

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noisy sa-omit maps in solvent region.
by Francis E Reyes 19 Jan '12

19 Jan '12

Hi phenixers I'm calculating a composite sa-omit map for my entire molecule at 4 A. While my molecule more or less has density (very good for backbone, not so much for sidechains), the solvent region seems to be particularly noisy. Is this the normal experience for composite sa-omit maps at this resolution? I'm particularly interested in what autobuild does when it 'stitches' the individual maps together, is it a direct stitch of the 2fo-fc's after refinement or is there some kind of real space density modification involved? Or a combination of both? Any suggestions appreciated, F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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