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Fwd: Refinement using new Phenix causes electron density/model mismatch
by Miles Pufall 12 Jan '09

12 Jan '09

The bb bounced my email back because the enclosures were too big - let me know if you'd like them. Thanks - Miles Begin forwarded message: > From: Miles Pufall <mpufall(a)cmp.ucsf.edu> > Date: January 12, 2009 12:16:06 PM PST > To: phenixbb(a)phenix-online.org > Subject: Refinement using new Phenix causes electron density/model > mismatch > > Hi Guys - > > I am having a very puzzling problem using the new Phenix (1.4-3). I > have about 20 structures that I am preparing to deposit with an > accepted manuscript, and decided to do a final refine using the > phenix.refine_gui not only to see if I got better numbers, but to > use the integrated validation tools, which I love. Unfortunately, > often, but not always, when I refine the pdb against the > *_refine_data.mtz the statistics are a bit worse, and when I open > the resulting *.map_coeffs.mtz in Coot it appears to be shifted with > tons of negative electron density. Needless to say, this is making > my nervous, so I've tried a few things: > > 1) Tried refining the same .pdb and .mtz files in Refmac - I seem > to get the same shifting. > 2) Try using the old .def file left over from the final run (just > to make sure I didn't screw up some setting) - and I get the same > shifting. > 3) Try refining against the original .sca file - and I get the same > shifting. > 4) Try molecular replacement of the refined .pdb against the > original .sca file - and sometimes, but not always, get a shift. > > I am nervous and concerned - can you help me figure out what > happened? I am enclosing an example - > > refine_001.pdb = pdb I refined in new phenix > refine_001map_coeffs.mtz = mtz output from new phenix refinement > (lots of red) > oste44a_output.sca = original scale file from HKL2000 > MR.1_refine_data.mtz = data from which I am refining > sgk_ost_temp_H_refine_004.pdb > > Thanks - > > Miles > > Miles Pufall > Postdoctoral Scholar > Yamamoto Lab > UC San Francisco > Cellular and Molecular Pharmacology > Mail Stop 2280 > 600 16th Street, Genentech Hall S-574 > San Francisco, California 94158-2517 > (415)476-4480 > > Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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Deadline for ALS PX beamtime this Thursday, Jan 15.
by Peter Zwart 12 Jan '09

12 Jan '09

Dear All, The deadline for general user proposals for PX beamtime at the ALS is coming up soon (Jan 15)! At the BCSB, we have 5 beamlines for which you can apply for beamtime. At the Berkeley Center for Structural Biology (BCSB) we have recently completed a number of upgrades: Sector 8: Recent improvements include: * A high-accuracy microdiffractometer on BL 8.2.1, allowing for centering and viewing of very small crystals * Robotic automounters which can increase the screening throughput at the beamlines, and allows for the implementation of remote data collection. * A new large format (315mm active surface area) CCD detector on BL 8.2.1, facilitating data collection on large unit cell crystals Sector 5: Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. Beamline 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. Remote data collection for general users on sector 5 is currently being tested for a limited number of users. Please contact beamline staff for details. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for next round of beamtime (March-April) at the Advanced Light Source, please submit a General User proposal by Januari 15, 2009. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. (Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime.) ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Re: [phenixbb] TLS in phenix.refine_gui
by Pavel Afonine 11 Jan '09

11 Jan '09

Hi Miles, > Thanks for the info. I see where I can load a parameter file in the > gui (File => Open parameter file) but I don't think I have it with the > right extension (.eff or .param). I'll give it a whirl tomorrow. Oh good, I'm glad to hear that this exists! I'm not sure if it relies on the file extension (it wouldn't be right if it does). I think we should have this option (to load a parameters file) right next to the prompt for PDB, data and CIF files. Best, Pavel.

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Scratch last help request
by Miles Pufall 11 Jan '09

11 Jan '09

As it turns out there were some problems with my .pdb file - missing chain label somehow. Once I fixed it everything works - sorry for the trouble. Miles Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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Error running refine_gui
by Miles Pufall 10 Jan '09

10 Jan '09

Hi Guys - I was running the phenix_gui ad had just started a refinement run with tls, adp, occupancy, individual sites, simulated annealing, update waters and add hydrogen when the run stop and this error popped up: RuntimeError : mean_weighted() argument is an empty array Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 259, in OnExcept raise event.data RuntimeError: mean_weighted() argument is an empty array CHeers - M Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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Postdoc Crystallographer Position - Berkeley
by Paul Adams 10 Jan '09

10 Jan '09

Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 22539 Division: Physical Biosciences Date Opened: 1/5/2009 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. Administrator: Kristine Sawyer [ KKSawyer(a)lbl.gov ][ 1-510-486-4151 ] --

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phenix v1.4-3 and NX
by Jesper Lykkegaard Karlsen 10 Jan '09

10 Jan '09

Hi, After upgrading our workstations to phenix v1.4-3, the user started having problems connecting to the machines through nxclient. The login ended up with a black screen on the client and absolutely no error messages on neither client nor server. The problem seemed to come from setting up the global environment for phenix (phenix_env.sh). I narrowed the problematic statement down to this: /if [ "$PHENIX_MTYPE" = "unknown-unknown" ]; then exit 1 fi/ Although "$PHENIX_MTYPE" = "intel-linux-2.6-x86_64" when logged in, somehow the "nx user" gets "$PHENIX_MTYPE" = "unknown-unknown" when it logs in, through it's authorization key, to establish the users session. To make a already to long story short. The problem can be fixed by commenting out the problematic statement above. And one question to the developers: Could this be avoided in the future? Perhaps give a warning instead off exiting completly! Sincerely Jesper -- Jesper L. Karlsen Scientific Computing Centre for Structural Biology Department of Molecular Biology University of Aarhus Gustav Wieds Vej 10C 8000 Aarhus C Phone: +45 8942 5268 E-mail: jelka(a)bioxray.au.dk

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Re: [phenixbb] phenix v1.4-3 and NX
by Jesper Lykkegaard Karlsen 09 Jan '09

09 Jan '09

Hi Paul, > what happens if you change the statement to say: > > exit 0 > > instead of exit 1? No did not help, still get black screen on the nxclient. Only out-commenting/deleting helps. Cheers, Jesper > > On Jan 9, 2009, at 3:52 AM, Jesper Lykkegaard Karlsen wrote: > >> Hi, >> >> After upgrading our workstations to phenix v1.4-3, the user started >> having problems connecting to the machines through nxclient. The >> login ended up with a black screen on the client and absolutely no >> error messages on neither client nor server. >> >> The problem seemed to come from setting up the global environment for >> phenix (phenix_env.sh). I narrowed the problematic statement down to >> this: >> >> if [ "$PHENIX_MTYPE" = "unknown-unknown" ]; then >> exit 1 >> fi >> >> Although "$PHENIX_MTYPE" = "intel-linux-2.6-x86_64" when logged in, >> somehow the "nx user" gets "$PHENIX_MTYPE" = "unknown-unknown" when >> it logs in, through it's authorization key, to establish the users >> session. >> >> To make a already to long story short. The problem can be fixed by >> commenting out the problematic statement above. >> >> And one question to the developers: >> >> Could this be avoided in the future? >> Perhaps give a warning instead off exiting completly! >> >> Sincerely >> Jesper >> >> -- Jesper L. Karlsen Scientific Computing Centre for Structural >> Biology Department of Molecular Biology University of Aarhus Gustav >> Wieds Vej 10C 8000 Aarhus C Phone: +45 8942 5268 E-mail: >> jelka(a)bioxray.au.dk_______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >

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fixing a partial solution of mol. rep.
by chern 07 Jan '09

07 Jan '09

I am doing a molecular replacement. There are two types of protein molecules in the crystal. One type is forming a hexameric core; there are 6 molecules of the second type that I need to locate. I found a solution for the hexameric core, but the other 6 molecules are difficult to find. 1. Can I fix the solution for the core, so that I don't have to find it every time. The other inconvenience with that is that the origine is different for every new run. If I fix the hexamer, then I fix the origine. It's important to me to compare different runs of MR. 2. Some of the six other molecules that MR finds are not the closest to the core. How can I request to output the closest molecules? Maia

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TRIED resolve ...NEED A BIGGER VERSION... message
by Ben Eisenbraun 05 Jan '09

05 Jan '09

Howdy Phenixians, One of my users is running phenix.autobuild, and while it seems to run okay, the output contains this warning: TRIED resolve ...NEED A BIGGER VERSION... Looking through phenix/phenix/autosol/run_resolve.py, it seems like this is an informational message, but I'm not sure, so I figured I'd ask. Is this actually an error? This is phenix-1.3-final on OS X 10.5. Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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