- phenixbb - phenix-online.org

rmsd: phenix vs refmac
by Frank von Delft 25 Jan '09

25 Jan '09

Hi I thought that a while ago, I read somewhere that rmsd(bonds) had not been calculated the same way in phenix as in refmac. I believe it was in connection with automated weights, and that rmsd(bonds) always much lower in phenix. I understood too that this had been adjusted since to match refmac. But we're still seeing some much lower rmsd(bond) from phenix: in particular, when we take a refmac model and plug it straight into phenix, the rmsd for cycle zero is already much lower than what it was at the end of refmac. Could someone enlighten...? (Yup, latest version of phenix.) Thanks! phx

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bond and angle rmsds: phenix.refine, Refmac, hydrogens, ...
by Pavel Afonine 25 Jan '09

25 Jan '09

For all who asked about observed differences in bond rmsd reported by phenix.refine and Refmac, H atoms included in statistics calculation and more... 1) First, I wanted to check bond rmsd reported by phenix.refine. I made up a PDB file containing just one residue (SER, no H atoms) and I wrote a crystal-clear and simple Python script that computes bond rmsd for this residue. Here are the numbers: Bond length rmsd: Script: 0.148 phenix.pdbtools: 0.148 phenix.refine: 0.148 Refmac_5.5.0070: 0.152 Both programs are using the Monomer Library. Since both of these very different ways of computing bond rmsd: this simple script and phenix.refine, give the identical values, I tend to think that the PHENIX implementation is actually correct. I have no idea why Refmac gives a different value and I think it's now up to Refmac developers (or any other enthusiast) to find it out or show that I'm wrong in my calculations. It well could also be me who's incorrectly using Refmac - today was my second time I tried it (the first was 3 or 4 years ago) -:) As for the bond angles rmsd, I didn't bother to include it into the script, but for the rest of tools in question, the numbers are: phenix.pdbtools: 16.628 phenix.refine: 16.628 Refmac_5.5.0070: 16.628 so all results seem to be in-sync. 2) Some people reported that the geometry statistics for the exact same structure with and without hydrogens seems to be reported different in phenix.refine. To find out, I did the same test as above, where I used the same one residue model with all hydrogens added. Unfortunately, I failed to make Refmac accept a PDB file containing H atoms so I gave up after 20 minutes of struggle. Here are the numbers: Bond length rmsd: Script: 0.155 phenix.pdbtools: 0.155 phenix.refine: 0.155 So, it seems like the hydrogens are included... I have to fix it. Well at least those who are doing refinement using neutron data or both X-ray and neutron data, were not concerned, since in that case I presume the H and D atoms should be included. Anyway, I'm fixing it right now, I'm making a corresponding regression test (to make sure the fix stays there forever) and the fixed version will be available in the next release. By the way, the new tool, phenix.model_vs_data is and was smart about this: it automatically excludes H and D atoms if X-ray data is used. And this proves it: phenix.model_vs_data: 0.148 which is the exact same number as in "1)", where H were not present. Thanks to all who raised this issue (Frank von Delft, Jianghai Zhu, Karolina Michalska and others)! Pavel. PS> All files used and the script are here: http://cci.lbl.gov/~afonine/rmsd_issue/ Use "phenix.python run.py" to run the script.

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IAS causes phenix.refine to die
by Anna Gardberg 24 Jan '09

24 Jan '09

Dear phenix list, My 0.75 A refinement has some problems in its higher resolution bins, so I thought I might try adding in IAS scatterers. However, the phenix.refine (version 2008_09_13_0905) crashed when I set "ias = True". I hope someone here can help me figure out the problem. I include snippets of output below, as the entire error message was very lengthy. Am I misusing the command, is there a problem with my system setup, or what? Regards, Anna Gardberg ----------Building IAS model---------- >>> Adding IAS.......... Total number of covalent bonds = 895 show_stack(1): /home/a1g/downloads/cci_apps_sources/mmtbx/ias/__init__.py(438) _ _init__ show_stack(2): /home/a1g/downloads/cci_apps_sources/mmtbx/ias/__init__.py(371) s et_peaks show_stack(3): /home/a1g/downloads/cci_apps_sources/mmtbx/ias/__init__.py(616) _ _init__ show_stack(4): /home/a1g/downloads/cci_apps_sources/mmtbx/model.py(494) add_ias show_stack(5): /home/a1g/downloads/cci_apps_sources/phenix/phenix/refinement/str ategies.py(409) refinement_machine show_stack(6): /home/a1g/downloads/cci_apps_sources/phenix/phenix/refinement/dri ver.py(1082) run <snip pages of output> /home/a1g/downloads/cci_apps_build/lib/cctbx_maptbx_ext.so(boost::python::obje cts::make_holder<4>::apply<boost::python::objects::value_holder<cctbx::maptbx::o ne_gaussian_peak_approximation>, boost::mpl::vector4<scitbx::af::const_ref<doubl e, scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double, scitbx::a f::trivial_accessor> const&, bool const&, bool const&> >::execute(_object*, scit bx::af::const_ref<double, scitbx::af::trivial_accessor> const&, scitbx::af::cons t_ref<double, scitbx::af::trivial_accessor> const&, bool const&, bool const&)+0x 75c) [0x2a9d79598c] /home/a1g/downloads/cci_apps_build/lib/cctbx_maptbx_ext.so(cctbx::maptbx::find _gaussian_parameters::find_gaussian_parameters(scitbx::af::const_ref<double, sci tbx::af::trivial_accessor> const&, scitbx::af::const_ref<double, scitbx::af::tri vial_accessor> const&, double const&, double const&, double)+0x3fe) [0x2a9d7827f e] /lib64/tls/libm.so.6 [0x32ee506263] /lib64/tls/libc.so.6 [0x32ee22e300] Floating-point error (Python and libc call stacks above) [1]+ Done gedit newscale-ias.eff

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Unmasking cavities
by Frank von Delft 23 Jan '09

23 Jan '09

Hi After being through phenix.refine, I see in my hydrophobic core a big space (a few atoms wide) that is filled with strong negative difference density. I suspect the culprit is the bulk solvent mask, which is defined too tightly. The online manual mentions three parameters, but not what they do. solvent_radius, shrink_truncation_radius, grid_step_factor What *exactly* do they do? (I thought I'd elicit a contribution for the online docs this way :) Cheers phx

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geometry of disulfide and NAG
by Li-Zhi Mi 22 Jan '09

22 Jan '09

Hi, I am using phenix to refine a low resolution structure. The problem I had is that the geometry of disulfide and NAG in the refined structure is not right. I did use a very tight geometry restrains. Both wxc_scale and wxu_scale are set to 0.05. In the refined structures, the sulfur of one cys is very close to the Cb of its disulfide partner. For NAG part, C2-N2-C7-O7-C8 should be in the same plane. But they are not. Is there a way to adjust these violations? Thanks in advance for the helps, Li-Zhi Mi,

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HL A B C D
by Raja Dey 21 Jan '09

21 Jan '09

Hello, If I want to use F, SigF and HLA, B, C and D in the phenix refinement, should I use the same command like phenix.refine data.mtz model.pdb, where data.mtz contains FREER, F, SIGF, HLA, HLB, HLC and HLD? How do I check that phenix.refine used the HL coefficients? Looking forward to hearing from you... Thanks... Raja

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Disappearing side chains after autobuilding
by Katya Heldwein 21 Jan '09

21 Jan '09

Hi, I ran phenix.autobuild with default setting (rebuild_in_place), and noticed that some side chains were gone in the resulting overall_best.pdb. That is, let's say, I started with Phe as residue 10. After rebuilding, the Phe10 is still called Phe in the output file, but the side chain atoms are gone, leaving residue 10 as Ala. This happened for several side chains, and I am at a loss for why this happened. Is this some kind of a bug? 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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missing map coefficients
by Anne Mølgaard 15 Jan '09

15 Jan '09

I am new to Phenix, so there might be an easy explanation for this problem, though I have not been able to find a solution in the documentation. I am using phenix version 1.3b-rc4, intel-linux-2.6. I have solved a structure using phenix.automr, followed by phenix.autobuild (run from command line using "phenix.autobuild data=fromXDS_unique.mtz model=AutoMR_run_2_/MR.1.pdb seq_file=sequence.fas"). The program runs succesfully, and I get the output files I should expect. However, the overall_best_refine_map_coeffs.mtz does not contain the map coefficients 2FOFCWT PH2FOFCWT for the 2mFo-DFc map and FOFC and PHFOFC for the Fo-Fc difference map. mtzdmp gives me the following columns: 1 ASC 0 28 0 100.00 10.6 10.6 28.28 1.85 H H 2 NONE 0 35 0 100.00 13.3 13.3 28.28 1.85 H K 3 NONE 0 71 0 100.00 26.6 26.6 28.28 1.85 H L 4 NONE 1.0 1888.8 0 100.00 148.71 148.71 28.28 1.85 F FP 5 BOTH 1.0 1.0 0 100.00 1.00 1.00 28.28 1.85 Q SIGFP 6 NONE -180.0 180.0 0 100.00 2.08 90.23 28.28 1.85 P PHIM 7 BOTH 1.000 1.000 0 100.00 1.000 1.000 28.28 1.85 W FOMM 8 NONE .0 19.0 0 100.00 9.50 9.50 28.28 1.85 I FreeR_flag 9 BOTH .0 .0 0 100.00 .00 .00 28.28 1.85 F FC What should I do to get these map coefficients? Thanks for your help! Best regards, Anne

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Will phenix.refine read CNS *.cv files?
by Scott Classen 15 Jan '09

15 Jan '09

Hi all, I'm embarking on a collaboration with someone who is providing me with CNS cross validated data files. They look something like this. NREFlection= 92086 ANOMalous=FALSe { equiv. to HERMitian=TRUE} DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END INDE 3 0 0 FOBS= 100.142 SIGMA= 1.478 IOBS= 10028.400 SIGI= 293.800 TEST= 0 INDE 4 0 0 FOBS= 158.996 SIGMA= 2.329 IOBS= 25279.600 SIGI= 735.200 TEST= 0 INDE 5 0 0 FOBS= 492.449 SIGMA= 17.677 IOBS= 0.242506E+06 SIGI= 17098.000 TEST= 0 INDE 7 0 0 FOBS= 246.492 SIGMA= 3.127 IOBS= 60758.400 SIGI= 1531.800 TEST= 0 INDE 8 0 0 FOBS= 32.790 SIGMA= 0.549 IOBS= 1075.200 SIGI= 35.700 TEST= 1 INDE 9 0 0 FOBS= 426.866 SIGMA= 8.886 IOBS= 0.182215E+06 SIGI= 7507.000 TEST= 0 INDE 10 0 0 FOBS= 411.347 SIGMA= 8.597 IOBS= 0.169206E+06 SIGI= 6999.000 TEST= 0 INDE 11 0 0 FOBS= 87.275 SIGMA= 1.346 IOBS= 7617.000 SIGI= 233.200 TEST= 0 When I try to run phenix.refine --dry_run my_model.pdb my_CNS_cv_file.cv I get the following error: Processing inputs. This may take a minute or two. Sorry: Unknown file format: my_CNS_cv_file.cv Any ideas? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [phenixbb] Will phenix.refine read CNS *.cv files?
by Scott Classen 15 Jan '09

15 Jan '09

Hi Nick, I think I tried that at some point, but the problem lies in the IOBS. Some are regular float fortran format: INDE 3 0 0 FOBS= 100.142 SIGMA= 1.478 IOBS= 10028.400 SIGI= 293.800 TEST= 0 while other IOBS are large and for some reason CNS decided to put them in scientific notation such as INDE 5 0 0 FOBS= 492.449 SIGMA= 17.677 IOBS= 0.242506E+06 SIGI= 17098.000 TEST= 0 As far as I can tell this requires two sets of fortran format statements for f2mtz to work properly. format '(6X,3F5.0,6X,F10.3,7X,F10.3,6X,E15.3,/,24X,F10.3,6X,F10.0)' or format '(6X,3F5.0,6X,F10.3,7X,F10.3,6X,F10.3,/,24X,F10.3,6X,F10.0)' I'm playing around with with grep to separate the original cv file into reflections with IOBS in F10.3 format and those with IOBS in E15.3 format, convert with f2mtz, then CAD them together, but this is bloody cumbersome. I was hoping phenix.refine would just automagically figure it all out. Scott On Jan 14, 2009, at 5:35 PM, Noinaj, Nicholas (NIH/NIDDK) [F] wrote: > Scott, > > <not sure if anyone has remedied your problem yet> > > I don't know if you can read cns file directly into phenix.refine. > but > here is another option....convert the cns file to *.mtz using CCP4. > If > you use the CCP4i GUI --> Reflection Data utilities --> Convert > to/modify/extend MTZ. You can also retain the original flagged > reflections here also. You can then use the *.mtz file in > phenix.refine. > > If you need further help, just drop me a quick email. I can also > try it > here if you supply me with the data file, but this may be too 'top > secret' (lol). Best of Luck! > > > > > > Cheers, > Nick > > > > -----Original Message----- > From: Scott Classen [mailto:[email protected]] > Sent: Wednesday, January 14, 2009 8:06 PM > To: PHENIX user mailing list > Subject: [phenixbb] Will phenix.refine read CNS *.cv files? > > Hi all, > I'm embarking on a collaboration with someone who is providing me with > CNS cross validated data files. They look something like this. > > > NREFlection= 92086 > ANOMalous=FALSe { equiv. to HERMitian=TRUE} > DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END > INDE 3 0 0 FOBS= 100.142 SIGMA= 1.478 IOBS= 10028.400 > SIGI= 293.800 TEST= 0 > INDE 4 0 0 FOBS= 158.996 SIGMA= 2.329 IOBS= 25279.600 > SIGI= 735.200 TEST= 0 > INDE 5 0 0 FOBS= 492.449 SIGMA= 17.677 IOBS= > 0.242506E+06 > SIGI= 17098.000 TEST= 0 > INDE 7 0 0 FOBS= 246.492 SIGMA= 3.127 IOBS= 60758.400 > SIGI= 1531.800 TEST= 0 > INDE 8 0 0 FOBS= 32.790 SIGMA= 0.549 IOBS= 1075.200 > SIGI= 35.700 TEST= 1 > INDE 9 0 0 FOBS= 426.866 SIGMA= 8.886 IOBS= > 0.182215E+06 > SIGI= 7507.000 TEST= 0 > INDE 10 0 0 FOBS= 411.347 SIGMA= 8.597 IOBS= > 0.169206E+06 > SIGI= 6999.000 TEST= 0 > INDE 11 0 0 FOBS= 87.275 SIGMA= 1.346 IOBS= 7617.000 > SIGI= 233.200 TEST= 0 > > When I try to run phenix.refine --dry_run my_model.pdb > my_CNS_cv_file.cv > > I get the following error: > > Processing inputs. This may take a minute or two. > Sorry: Unknown file format: my_CNS_cv_file.cv > > > Any ideas? > > Thanks, > Scott > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Scott Classen, Ph.D. > SIBYLS Beamline 12.3.1 > http://bl1231.als.lbl.gov > Advanced Light Source > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd > MS6R2100 > Berkeley, CA 94720 > C) 510.206.4418 > O) 510.495.2697 > Beamline) 510.495.2134 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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f_prime and f_double_prime in MIRAS/SIRAS
by Leo Sazanov 14 Jan '09

14 Jan '09

Hi, how can one enter f_prime and f_double_prime values for SIRAS/MIRAS experiments in phenix.autosol? Could not find any examples of that in manual, only for MAD. Just putting them in as f_prime=... and f_double_prime=... does not work, it then assumes MAD experiment. Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-dunn.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Jan 15th deadline - User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 Jan '09

14 Jan '09

Dear Users, /Deadline for March/April 2009 proposals will be Jan 15, 2009. / Through the Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source, scientists can send protein crystals to Berkeley Center for Structural biology (BCSB) staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Click on "protein crystallography" to begin proposal. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for March/April 2009 allocation period, proposals must be submitted by January 15, 2009. The deadline for CC proposals for the time period May/June 2009 will be March 15, 2009. Regards, Banumathi Sankaran

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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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question about xn joint refinement
by crystallogrphy 03 Jan '09

03 Jan '09

Deall all: I have a question about xray and neutron joint refinement. When I start phenix joint refinement like this, phenix gave the wrong message: phenix.refine dhfr-mtx-rt-xray.hkl neutron_data.file_name=newdhfr_un_change.hkl xn_easy_080326a.pdb input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn xray_data.r_free_flags.generate=True neutron_data.r_free_flags.generate=True refine_default.params ===================== joint neutron/xray refinement start ===================== Traceback (most recent call last): call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3-rc4/phenix/phenix/refinement/driver.py", line 1031, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3-rc4/phenix/phenix/refinement/strategies.py", line 184, in refinement_machine * assert not neutron_refinement AssertionError* I guess in my default parameters, something is wrong, particularly the bold word I highlighted. But I do not know how to fix. Does any one have a clue?\ Thanks and Happy New Year! main { bulk_solvent_and_scale = True simulated_annealing = False ordered_solvent = False ncs = False ias = False number_of_macro_cycles = 3 max_number_of_iterations = 25 use_form_factor_weights = False tan_u_iso = False use_convergence_test = False target = *ml mlhl ml_sad ls min_number_of_test_set_reflections_for_max_likelihood_target = 50 max_number_of_resolution_bins = 30 reference_xray_structure = None use_experimental_phases = None compute_optimal_errors = False random_seed = 2679941 *scattering_table = wk1995 it1992 *n_gaussian neutron* use_normalized_geometry_target = True target_weights_only = False use_f_model_scaled = False max_d_min = 0.25 fake_f_obs = False -- 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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Error
by Miles Pufall 27 Dec '08

27 Dec '08

Hi - It appears there was a problem with the NCS flag being on, and when I took it off I received this error. Let me know if you'd like data to recreate this. Cheers - Miles RuntimeError : OpenGL: invalid operation Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 188, in run self.check_params_and_run() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 229, in check_params_and_run self.model.add_hydrogens() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Model.py", line 369, in add_hydrogens self.update_from_interface() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Model.py", line 181, in update_from_interface self.update_viewer() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Model.py", line 317, in update_viewer self .viewer_frame.glview.update_structure_from_files(self.get_all_files()) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 166, in update_structure_from_files self.update_structure(pdb_hierarchy, atomic_bonds, redraw=True) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 180, in update_structure self.OnUpdate(recenter=True) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 208, in OnUpdate self.update_view(True, True) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 566, in update_view self.OnRedraw() File "/usr/local/phenix-1.4-3/gltbx/wx_viewer.py", line 473, in OnRedraw self.OnRedrawGL(event) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 118, in OnRedrawGL wx_viewer.wxGLWindow.OnRedrawGL(self, event) File "/usr/local/phenix-1.4-3/gltbx/wx_viewer.py", line 476, in OnRedrawGL gltbx.util.handle_error() RuntimeError: OpenGL: invalid operation 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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PHENIX 1.4-3 Available
by Paul Adams 23 Dec '08

23 Dec '08

= = = = = ======================================================================== PHENIX 1.4-3 Development Release = = = = = ======================================================================== The PHENIX developers are pleased to announce that the 1.4-3 development version of PHENIX is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ This version of PHENIX includes the following new features: - A new GUI for phenix.xtriage: - To start the GUI version type phenix.xtriage_gui - A new GUI for phenix.refine: - To start the GUI version type phenix.refine_gui - Incorporates a subset of Molprobity validation tools - Documentation for the new GUIs: - See the help menu or button after starting the GUI - Structure refinement (phenix.refine) - Default is to fill missing reflections in map calculations with DFc - Default is to write phase combined maps if experimental phases are used in refinement - Improved capabilities for selection of atoms for occupancy refinement - Xplor maps no longer written by default - Numerous minor bug fixes - Multi-crystal averaging (phenix.multi_crystal_average) - Fast secondary structure building (phenix.find_helices_strands) - Find all ligands in a map (phenix.find_all_ligands) - Minor bug fixes in phenix.elbow and phenix.reel Full documentation is available here: http://www.phenix-online.org/documentation/ There is a PHENIX bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to PHENIX should visit the PHENIX website for information about the PHENIX Industrial Consortium. The development of PHENIX is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the PHENIX Industrial Consortium. = = = = = ======================================================================== PHENIX 1.4-3 Development Release = = = = = ======================================================================== -- 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: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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