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Spermine molecule on a crystallographic two-fold axis
by Marjolein Thunnissen 26 Mar '09

26 Mar '09

I have been trying to find in the documentation if there is a way to do this but I have the following problem: In a recent structure we are currently refining we identified a spermine molecule sitting right on a crystallographic two-fold axis. Spermine has internal two-fold symmetry and it is part of extensive crystal contacts. I just wonder how to refine this with Phenix. In Refmac it is easy, I put the occupancies to 0.5 and the program ignores the clashes of the symmetry related molecule, but that doesn't seem to be the way that Phenix works. Can anyone give me advise on this? Thanks __________________________________________________________________________ | Marjolein Thunnissen Phone +46-(0)46-22 24584| | Associate Professor Fax +46-(0)46-22 24692| | Dept of Molecular Biophysics, Lund University http://www.mbfys.lu.se | | PO-Box 124 S-221 00 Lund, Sweden | | | |Scientific Coordinator I911 (Max-lab): MAD and fixed-wavelength stations | | for macromolecular crystallography | |__________________________________________________________________________|

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twin refine error message
by Alex Taylor 26 Mar '09

26 Mar '09

Hi, I am trying to refine using the following twin operators output from xtriage for C2221 1/2*h-1/2*k,-3/2*h-1/2*k,-l 1/2*h+1/2*k,3/2*h-1/2*k,-l but phenix.refine (vers 1.4-4 and 1.4-3) fails with the following error message: =============================== refinement start ============================== Traceback (most recent call last): File "/usr/progs/linux/phenix-1.4-4/phenix/phenix/command_line/refine.py", line 18, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/progs/linux/phenix-1.4-4/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/progs/linux/phenix-1.4-4/phenix/phenix/refinement/driver.py", line 1121, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/progs/linux/phenix-1.4-4/phenix/phenix/refinement/strategies.py", line 191, in refinement_machine twin_law = sgtbx.rt_mx( params.twinning.twin_law ) RuntimeError: cctbx InternalError: /net/anaconda/scratch1/phenix/phenix-1.4-4/cctbx_project/cctbx/sgtbx/rt_mx.cpp(230): Unsuitable value for rational rotation matrix. I am running the RedHat WS 5.2 64-bit OS. Thanks for suggestions, Alex -- Alex Taylor, Ph.D. Technical Director, X-ray Crystallography Core Laboratory University of Texas Health Science Center at San Antonio Office: 210-567-3781 FAX: 210-567-6595

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Postdoc Crystallographer Position - Berkeley
by Paul Adams 24 Mar '09

24 Mar '09

Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 22539 Division: Physical Biosciences Date Opened: 3/24/2009 Summary: A postdoctoral position is immediately available to study structure and function of macromolecular complexes and enzymes using X-ray crystallographic methods. This position is joint between the Center for Protein Folding Machinery (www.proteinfoldingcenter.org) and the Joint BioEnergy Institute (www.jbei.org). Robotic hardware for performing crystallization trials and imaging results are available. Crystals will be characterized and data collected using the beamline resources of the Berkeley Center for Structural Biology at the Advanced Light Source. The biological systems to be studied are: - Type-II chaperonins responsible for the refolding of unfolded proteins in archeal and mammalian cells. - Glycosyl transferases responsible for the synthesis of hemicellulose in plants. - Novel glycosyl hydrolases that are able to breakdown cellulosic material for biofuels production. Duties: Using robotic hardware to perform screens for crystallization conditions. Optimization of crystallization conditions. Biophysical characterization of protein samples using standard techniques, such as dynamic light scattering. Characterization of crystals using the Berkeley Center for Structural Biology beamlines at the Advanced Light Source. Collection and analysis of diffraction data, model building and structure refinement. Extensive email and verbal interaction with other researchers. Qualifications: Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using crystallographic methods. Experience with crystallization methods. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Note that this is a one-year appointment with renewal based on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit http://cjo.lbl.gov/ and search for the job number 22539 or visit: http://jobs.lbl.gov/LBNLCareers/details.asp?jid=22539&p=1 -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

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refinement with a covalent inhibitor.
by Maia Cherney 24 Mar '09

24 Mar '09

Hi all, I am trying to refine a complex with a covalent inhibitor (E-64) that has a carboxylate group. My model has it planar, but after refinement the two oxygens of the carboxyl group get out of the plane. In the cif file generated by elbow this plane description is missing, I added it manually, but the result is the same. Maia

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ADP settings for protein and solvent
by Katya Heldwein 23 Mar '09

23 Mar '09

Hi, I'd like to refine group adps for my protein and individual adps for the solvent while refining coordinates for all atoms. How can I set that up in the command line mode? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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Question about scale of ED maps from phenix vs map coeffs when displayed in COOT
by Schubert, Carsten [PRDUS] 21 Mar '09

21 Mar '09

Hi, Sorry for the crosspost, but I am not sure were the problem is located: I noticed that the xplor maps generated by phenix seem to be on a different scale than the maps generated from the map-coefficients from the same refinement run when the maps-coeffs are read into coot. Usually I only read in the map-coeffs and the scale seems reasonable to me, i.e. average density ~0.28 e/A3 at 1 sigma for a 2fofc map. The map from the same run (converted to ccp4 map in mapman) is at 0.55e/A3 at 1 sigma, when displayed in coot. The map should be normalized in phenix (apply_sigma_scaling=True) and the stats from mapman indicate an RMS deviation of ~1. For fofc maps I need to crank up the display to 6 sigma to get an equivalently looking map as the one from the map-coefficients at 3 sigma contour level. Any hints as to were the factor of 2 comes from, coot or phenix? Cheers, Carsten

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Problems with phasing a protein (1300aa)
by Kumar 20 Mar '09

20 Mar '09

Hello Phenixbb members, I have been trying to obtain phases for a protein which contain ~1300aa. We have obtained native data to a resolution of 3.3A (Space group I222 or I212121). But we are having tough time phasing it. 'Se' labeled crystals diffracts maximally up to 3.5 to 4 A and dies very quickly on most of the beamlines. We have scanned at Se wavelength and it gives very strong signal as it contain ~45 Se in AU (1300 aa). It is difficult to collect a complete dataset (maximally we get 50-60 % completion with Rmerge ~15) out of one crystal on regular beamline. At microfocus beamline (APS), we were able to collect data in 3-4 batches and merge them to get a complete dataset (Rmerge ~18-20) out of one crystal. We used data collected on microfocus beamline (at peak wavelength) for locating heavy atom position using SHELXD, Solve and Phenix.hyss. SOlve and Phenix.hyss find very few heavy atom sites 1-5 whereas SHELX-CDE lists many but shows no difference in original and inverted (contrast and connectivity). Our phasing attempts with datasets obtained after merging two incomplete dataset from two different crystal has also been disappointing. My another worry is absolute value of average intensity, which seems to be quite low in most of the datasets. Below I have pasted last table of scale.log (HKL2000). Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac 50.00 7.53 45.4 1.6 1.3 1.295 0.055 0.047 7.53 5.98 11.4 1.3 1.3 0.672 0.135 0.114 5.98 5.23 11.2 1.6 1.6 0.643 0.171 0.152 5.23 4.75 16.8 2.0 1.9 0.736 0.148 0.118 4.75 4.41 18.8 2.2 2.2 0.739 0.143 0.132 4.41 4.15 14.6 2.4 2.4 0.653 0.190 0.175 4.15 3.94 11.3 2.5 2.5 0.582 0.247 0.226 3.94 3.77 10.1 2.8 2.8 0.511 0.280 0.191 3.77 3.63 8.0 3.1 3.1 0.450 0.315 0.285 3.63 3.50 7.6 3.3 3.2 0.483 0.311 0.270 All reflections 15.5 2.3 2.2 0.694 0.153 0.106 Now, I want you to help me by answering some of my queries: 1. Is it possible to get MAD/SAD phasing done from a dataset having more than 15% Rmerge and resolution in the range of 4 - 4.5 Ang? 2. Will a complete data set obtained from merging various batches(30-40 frames each) from one or more than one crystal will have proper anomalous signal for phasing? I am worried as weak anomalous signal may get lost while merging. 3. Will such a low value of average Intensities (as shown above from HKL scale log file) will be good enough for MAD/SAD phasing or I really need to improve crystal quality for stronger diffraction. 4. For MAD/SAD phasing, till what resolution we need to have anomalous signal ? Many of my datasets shows anomalous signal maximally up to 6-8 A (calculated using Phenix.xtriage). 5. Since I have low resolution (3.5 to 4 A)data, relatively high Rmerge (14-15%), lower value of average intensity, anomalous signal up to 6 A or so..... which programs will be more useful for heavy atom location and to prevent false positives from being selected? We have been also trying our luck with heavy atom soak but that also has not been very encouraging. I would appreciate any suggestions in this regard. Thanks in advance and sorry for such a long mail. Kumar

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question about generating cif and pdb file using elbow
by crystallogrphy 20 Mar '09

20 Mar '09

Hi, I am using phenix.elbow to generate pdb and cif files with the tripos format file: phenix.elbow --initial_geometry egcg.mol2 --opt --output="LIG" --pdb-ligand The input pdb file contains hydrogen atoms and the output pdb file also contains hydrogen atom. My crystal data only difftracted to 2.4A, so hydrogen atoms cannot be seen. In the refinement, my ligand should not contain hydrogen atoms. So I add one more option not to add hydrogen following the online phenix documentation: phenix.elbow --initial_geometry --write-hydrogens=False egcg.mol2 --opt --output="LIG" --pdb-ligand *However, the program failed. Does anyone know why?* Usage: phenix.elbow [options] *phenix.elbow: error: no such option: --write-hydrogens* -- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: qunwan1(a)gmail.com lab phone: 216-368-3337

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Problems with kicked maps in 1.4.3 or 1.4.4
by Schubert, Carsten [PRDUS] 20 Mar '09

20 Mar '09

Hi Pavel, I am having some problems with kicked maps. The job fails with a cryptic message: "Sorry Duplicate mtz_label_amplitudes: 2FOFCWT" and nothing gets written I noticed this in 1.4.3 a couple of days ago, just upgraded to 1.4.4, same problem. Running the same job w/o kicked maps enabled runs fine. Any ideas? Cheers, Carsten Here is a snipped of the .def file. output { prefix = "Prim_105_D6" serial = 4 serial_format = "%03d" write_eff_file = True write_geo_file = False write_def_file = True export_final_f_model = mtz cns write_maps = True write_map_coefficients = True } electron_density_maps { map_format = *xplor map_coefficients_format = *mtz phs suppress = None map { mtz_label_amplitudes = None mtz_label_phases = None likelihood_weighted = None obs_factor = None calc_factor = None kicked = False fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "FOFCWT_no_fill" mtz_label_phases = "PHFOFCWT_no_fill" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } anomalous_difference_map { mtz_label_amplitudes = "ANOM" mtz_label_phases = "PHANOM" } grid_resolution_factor = 0.25 region = *selection cell atom_selection = None atom_selection_buffer = 3 apply_sigma_scaling = True apply_volume_scaling = False }

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Re: [phenixbb] Can Phenix do MR with medium/low res EM models?
by Gino Cingolani 19 Mar '09

19 Mar '09

thanks Ed, I'll look it up.... I kind of tried something similar but never worked in my hands. I'll give it another try! By the way, the address of my house is 107 Ardsley Drive Dewitt 13214, NY. See you on Saturday 10 or so. Give me a call if you have problems 315 657 4805 Gino *********************************************************** Gino Cingolani, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology SUNY Upstate Medical University 750 E. Adams Street, Syracuse, NY, 13210 Tel. (315) 464 8744 Fax. (315) 464 8750 Email: cingolag(a)upstate.edu *********************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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