- phenixbb - phenix-online.org

Geometry problem with the ligand
by Jhon Thomas 29 Mar '09

29 Mar '09

Hello all I am working with a 3.0 A dataset, which binds with cAMP. I have refined the dataset with phenix (TLS+Group_adp) and followed by weight optimization. Though cAMP fit well in the density, validation tools (molprobity, procheck) suggest the bond angles and bond lengths of ligand of completely refined model is very bad(100% bad). Can anyone suggest what could be the problem with model or refinement? I will appreciate the suggestions. Thanks in advance John

3 2

weight optimization
by peter hudson 29 Mar '09

29 Mar '09

Hello all I am very new to this field. I am refining a dataset of 3.0A resolution. I want to perform the weight optimization. while weight optimisation, occupancy refinemnet is default. I donot want torefine the occupancy of any of the atoms from my model. How can i set to occupancy_refinemnet=false. I will appreciate the suggestions. Thanks in advance Peter

3 2

Re: [phenixbb] Question about scale of ED maps from phenix vs map coeffs when displayed in COOT
by Ralf W. Grosse-Kunstleve 28 Mar '09

28 Mar '09

For phenix maps: the sum is over the entire unit cell. Ralf > Is the sum over the asymmetric unit or the portion of space that > happened to be covered by the map? The result of this calculation > depends greatly on the amount of solvent region that is included in > the sum. > > Dale Tronrud > > Ralf W. Grosse-Kunstleve wrote: > >> That was (and is) always a mystery for me: when I look at two maps (both > >> coming from phenix.refine): > >> - one is computed in COOT from phenix.refine map coefficients, and > >> - another one displayed in PyMol using X-plor formatted map. > >> > >> To make both maps looking identical I have to draw them at different > >> sigma levels, sometime very different. This is true for both fo-fc and > >> 2fo-fc maps. > >> > >> I have some ideas but no any proofs so I don't want to put my > >> speculations to the bb. So, I have no answer... May be Ralf or Paul E...? > > > > Our "sigmas scaled maps" are simply divided by the "biased standard > > deviation": > > > > sqrt(sum((value-mean)**2) / n) > > > > The mean of our maps is usually zero, as we don't usually include F000. > > > > Ralf

3 2

Refinement error
by Katya Heldwein 27 Mar '09

27 Mar '09

Hi, I am getting the following error when I run phenix.refine. How can I get rid of it? Katya =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- show_stack(1): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/twinning/twin_f_model.py(1676) r_values show_stack(2): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/twinning/twin_f_model.py(1837) r_work show_stack(3): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/f_model.py(2249) __init__ show_stack(4): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/twinning/twin_f_model.py(1139) info show_stack(5): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/__init__.py(109) show_comprehensive show_stack(6): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/refinement/strategies.py(280) refinement_machine show_stack(7): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/refinement/driver.py(1121) run show_stack(8): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/refinement/command_line.py(89) run show_stack(9): /programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/command_line/refine.py(16) <module> Floating-point error (Python call stack 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. -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

4 3

AssertionError in twin refinement...
by Francis E Reyes 26 Mar '09

26 Mar '09

====================== bulk solvent modeling and scaling ====================== |--(resolution: 2.00 - 23.08 A; n_refl. = 24304)------------------------------| | | | r_work= 0.2462 r_free= 0.2706 ksol= 0.32 Bsol= 47.55 scale= 1.149 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-2.11,5.80,-3.69,0.00,-0.00,-0.00); trace/3= -0.00 | | | | maximum likelihood estimate for coordinate error: None A | | x-ray target function (twin_lsq_f) for work reflections: 0.346916 | | twin fraction: 0.03 twin operator: k,h,- l | | -----------------------------------------------------------------------------| ================== ordered solvent: location/analysis/update ================== Start model: number = 165 b_iso_min = 37.62 (limit = 1.00) b_iso_max = 70.26 (limit = 50.00) b_iso_mean = 49.33 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 1.00) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = 2.45 (limit = 1.80) dist_sol_mol_max = 4.94 (limit = 6.00) Filtered: number = 71 b_iso_min = 37.71 (limit = 1.00) b_iso_max = 49.89 (limit = 50.00) b_iso_mean = 45.14 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 1.00) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = 2.45 (limit = 1.80) dist_sol_mol_max = 3.99 (limit = 6.00) Traceback (most recent call last): File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/ refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/ command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/ driver.py", line 1081, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/ strategies.py", line 364, in refinement_machine log = log) File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/solvent/ ordered_solvent.py", line 159, in __init__ use_kick_map = self.params.use_kick_maps).peaks_mapped() File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/solvent/ ordered_solvent.py", line 332, in find_peaks log = self.log) File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line 85, in __init__ symmetry_flags = maptbx.use_space_group_symmetry) File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/twinning/ twin_f_model.py", line 2244, in electron_density_map "m_gradient") AssertionError phenix version is 1.3 final. Ideas? thanks! FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 7

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 | |__________________________________________________________________________|

2 1

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

2 1

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 ] --

1 0

refinement with a covalent inhibitor.
by Maia Cherney 23 Mar '09

23 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

4 11

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

2 1