- phenixbb - phenix-online.org

Gordon Research Seminar this July
by Bradley Hintze 26 Apr '16

26 Apr '16

Attention Young scientist in crystallography and diffraction. Are you a young scientist interested in the methods in crystallography? Do you want to deepen your understanding of instrumentation, different diffraction methods, data processing, phasing, structure solution, etc.? The Gordon Research Seminar and Conference for Diffraction Methods happens July 16 - 22 (for both) at Bates College in Maine. It is a unique opportunity to interact with the researchers actively developing the exciting many methods related to crystallography and beyond. The conference is relatively small allowing close association with all in attendance allowing participants to discuss methods with those in the know. The Gordon Research Seminar is a two-day event before the Conference for those early in their career, e.g. students, postdocs, and beginning industry folks. This space allows young scientist to interact, ask questions, and discuss their science with peers. If you are interested in deepening your understanding of the methods behind crystallography, please consider applying to both the Gordon Research Seminar and Conference on Diffraction Methods. For all the details, please see: <goog_1374816820> https://www.grc.org/programs.aspx?id=16486 Apply soon! Any questions? Simply reply to this email. Thanks GRC chairs, Rike Müller-Werkmeister and Bradley Hintze

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Coot does not start up with OS 10.11 El Capitan
by Benoît Masquida 22 Apr '16

22 Apr '16

Dear Phenix, The graphic window of coot does not open either launch from the shell or from Phenix GUI. Has anyone experienced (and solved) this problem on El Capitan (from Apple)? Thanks for your help. BM -- Benoît Masquida b.masquida(a)unistra.fr UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB - Plateforme de Biologie 4 Allée Konrad Roentgen 67081 STRASBOURG Cedex

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phenix.polder - tool for calculating omit maps by excluding bulk solvent
by Dorothee Liebschner 21 Apr '16

21 Apr '16

Dear phenix users, Starting from the nightly build dev-2356, a new tool for calculating ligand omit-maps, called 'polder', is included in phenix. Usage: phenix.polder model.pdb data.mtz selection='chain A and resseq 123’ Phenix.polder calculates omit maps for atom selections by preventing the bulk solvent mask to flood into the atom selection area and its vicinity. The tool can be useful in cases where the density of the selected atoms is weak and possibly obscured by bulk solvent. Polder produces less biased maps compared to procedures where the atom selection occupancy is set to zero, and the atoms are included in the solvent mask calculation (in that case, the resulting difference density can have similar shape than the selected atoms). Phenix.polder excludes a larger volume from the bulk solvent and therefore prevents misinterpreting bulk solvent density as omit density. If you want to know more about how the tool is working and to see some examples, have a look at the presentation file: https://www.phenix-online.org/presentations/phenix_polder.pdf. The documentation page can be found here: www.phenix-online.org/version_docs/dev-2356/reference/polder.html Best wishes, Dorothee

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fit_loops using loop_lib
by Greg Bowman 21 Apr '16

21 Apr '16

Hi all - I’m having a problem getting phenix.fit_loops to run using the loop library (loop_lib=True). The phenix.fit_loops seems to work fine without this keyword (I get a good solution for a test case), but I have 3A density and wanted to restrict solutions to the loop library for the poorer density regions. I am running this from the command line, with this input: phenix.fit_loops pdb_in=refine_35-delloop1170to1172.pdb mtz_in=refine_35.mtz \ seq_file=KRJmonomer.seq start=1170 end=1172 chain_id=B \ loop_lib=True >> fit_loops-1170to1172-looplibrary.log I am using OSX ElCapitan (10.11.3) and get this error: File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 962, in <module> fit_loops=fit_loops(args=sys.argv[1:]) File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 598, in __init__ target_time=target_time, File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 760, in run_fit target_time=target_time, File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/autosol/UserMethods.py", line 3671, in Build_fit_gaps starting_residue_number=starting_residue_number) File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/loop_lib/clustering.py", line 2063, in apply_clusters d=get_density_map(map_coeffs_array=map_coeffs_array) File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/utilities/get_density_map.py", line 54, in __init__ assert not map_coeffs_array.anomalous_flag() AssertionError The last lines of the log file are: Fitting loop with loop-library... loop_lib length (including 3 on each end): 9 DATABASE: /Applications/phenix-1.10.1-2155/modules/chem_data/loop_library/loops_9_2.5/loop_lib CLUSTER_FILE: split_clusters.pkl.gz Thanks, Greg

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clash_guard failure
by Bock, Tobias 20 Apr '16

20 Apr '16

Dear colleagues, I am trying to refine a protein-DNA complex. In this structure, 2 DNA double strands are present with 50% occupancy (or similar occupancy’s) and overlap at certain positions. Phenix.refine crashed due to a nonbonded interaction distance issue. To fix that, I tried to exclude the DNA strands using: pdb_interpretation { custom_nonbonded_symmetry_exclusions="chain E" custom_nonbonded_symmetry_exclusions="chain F" } Nevertheless, phenix.refine crashed with the same error message. Changing the “nonbonded_distance_threshold” works, but results in terrible statistics (since this applies for the complete structure, I guess). Is there a way to exclude only the DNA strands (in regard to the clash guard) or a similar approach to refine the structure? Thank you in advance for your help, Tobias ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" 50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50 Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Re: [phenixbb] Merging Already-Scaled MTZs
by Tim Gruene 20 Apr '16

20 Apr '16

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Jacob, I overlooked the s at mtz, i.e. I thought you wanted to re-merge a single data set. My apologize for this. Your question is correctly formulated and perfectly valid. I would try pointless (easy) or cad (a little tedious but more prone to work) followed with aimless and its keyword 'onlymerge'. Best regards, Tim On Wednesday, April 20, 2016 07:36:07 PM you wrote: > Depends on your definition of "merge." What verb would you use for the > process I am describing? > > JPK > > -----Original Message----- > From: Tim Gruene [mailto:[email protected]] > Sent: Wednesday, April 20, 2016 3:05 PM > To: phenixbb(a)phenix-online.org > Cc: Keller, Jacob > Subject: Re: [phenixbb] Merging Already-Scaled MTZs > > Dear Jacob, > > it is technically not possible to merge relfection data twice, unless you > change to a higher symmetry space group: merging means replacing symmetry > related reflections with their mean. > > For scaling this is different - couldn't you repeat the scaling step? I am > not sure if phenix contains data processing software, I thought it starts > at data analysis and structure solution. > > Cheers, > Tim > > On Wednesday, April 20, 2016 06:59:04 PM Keller, Jacob wrote: > > Dear Crystallographers, > > > > I guess it is bad practice to merge/scale already-merged/scaled mtz's, > > but I have a special reason for wanting to do so. Does anyone know how > > this can be done in Phenix? > > > > The reason is, if you're interested, that I want to detwin several > > different datasets to varying degrees, then merge them. > > > > JPK > > > > ******************************************* > > Jacob Pearson Keller, PhD > > Looger Lab/HHMI Janelia Research Campus > > 19700 Helix Dr, Ashburn, VA 20147 > > email: kellerj(a)janelia.hhmi.org > > ******************************************* > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > Unsubscribe: phenixbb-leave(a)phenix-online.org > > -- > -- > Paul Scherrer Institut > Tim Gruene > - persoenlich - > OFLC/102 > CH-5232 Villigen PSI > phone: +41 (0)56 310 5297 > > GPG Key ID = A46BEE1A - -- - -- Paul Scherrer Institut Tim Gruene - - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iD8DBQFXF9yHUxlJ7aRr7hoRArioAKDxnnJxNGZaAbV8PDmUprCJuvk7mwCg21jr wG0I05gbSvcFjrfzndkNRWY= =BHXV -----END PGP SIGNATURE-----

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Merging Already-Scaled MTZs
by Keller, Jacob 20 Apr '16

20 Apr '16

Dear Crystallographers, I guess it is bad practice to merge/scale already-merged/scaled mtz's, but I have a special reason for wanting to do so. Does anyone know how this can be done in Phenix? The reason is, if you're interested, that I want to detwin several different datasets to varying degrees, then merge them. JPK ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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Autobuild
by Sam Tang 20 Apr '16

20 Apr '16

Dear colleagues I have recently downloaded a Windows GUI version of Phenix 1.10.1-2155. When I used AutoBuild these few days it keeps turning out the following errors: Job 1 failed: child process stderr output: command: ['phenix.autobuild', 'C:\\Users\\pcshaw\\Desktop\\NPAproc\\B13_proc\\AutoBuild_run_4_\\TEMP0\\PARAMS_1.eff', 'write_run_directory_to_file="C:\\Users\\pcshaw\\Desktop\\NPAproc\\B13_proc\\AutoBuild_run_4_\\TEMP0\\INFO_FILE_1"'] Traceback (most recent call last): File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\build\..\modules\phenix\phenix/command_line\autobuild.py", line 228, in <module> run_autobuild=run_autobuild(args=sys.argv[1:]) File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 564, in __init__ self.RunWizard() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 2372, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 4626, in AutoBuild_rebuild_cycle_run refine_2fofc=refine_2fofc) File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 5500, in AutoBuild_resolve_with_model hklout=hklout,labin=labin) UnboundLocalError: local variable 'labin' referenced before assignment Could I please enquire if these are due to mis-setting of parameters or in fact problems related to my recent installation? Yet another question on my mind is, is AutoMR still supported in this Windows version? I can now no longer find it in the GUI while it used to be there in the 1.7 Mac version. Kind regards Sam Biochemistry Programme, School of Life Sciences, CUHK

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phenix output graphs
by Christian Roth 19 Apr '16

19 Apr '16

Hi Phenix-Team, there are some nice graphs produced for example after refinement. If I want to save such a graph (B-Factor histogram) as jpg or so, is that possible or do I have to save the values and redraw it outside phenix? The only plot I oculd save was the B-Fac plot per residue, which wouldn't be helpful in that case. Thanks for some insight. Cheers Christian

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questions/problems with tls_as_xyz routines
by David A Case 18 Apr '16

18 Apr '16

I'm trying to use tls_as_xyz, but having some problems. 1. In the paper describing this, Urzhumtsev et al, Acta Cryst D71:1668, 2015, there seems to be something wrong with Section 6.2, which describes results on PDB entry "1dqv", syanptotagmin III. The description says that there are two copies of the molecule in the asymmetric unit, and the resolution is 2.5 Ang. However, the file with this code in the RCSB (which is indeed syanptotagmin III) has one molecule per asymmetric unit, a single chain of 296 amino acids, rather than two chains of 97 amino acids, as in Tables 2 and 3 of the paper cited above; the resolution is 3.2 Ang. And it doesn't look anything like the picture of "1dqv" in Fig. 3a. So something looks wrong; does anyone know what system Section 6.2 is using? 2. I'm asking the above because I'm having trouble with my own applications, and was hoping to check that I could reproduce the results in the paper. Apropos of that, is there a test case or example for tls_as_xyz in the phenix distribution? [I'm not all that familiar with phenix, so apologies if I've missed the easy way to find this.] 3. Here is a summary of what is not working for me. (I don't expect anyone to debug this on such little information, but thought that someone on the list might have done some similar calculation.) a. I took a small domain (residues 6-61 from GB3, PDB code 2IGD), and used Ethan Merrit's lsq_tls_fit to obtain a set of TLS tensors that best fit the deposited ADP's. The statisitcs are pretty good, indicating (not surprisingly) that motions in this domain are well characterized as a rigid body--which is why I chose this system. I just used the CA atoms for this initial study. b. I used phenix.tls_as_xyz to compute an ensemble from the TLS matrices obtained in step a. c. I then computed ADP's from the ensemble, using tools from cpptraj in Amber, (or our own codes, which give the same results). But the extracted isotropic B factors (and the anisotropic components) are much larger than the input ones. So, the ensemble is giving me what I expected: a sampling of structures whose fluctuations arise from the input TLS matrices. I've done a fair amount of due diligence in trying to track down errors on my end, but I could be making a mistake on any one of the steps above. Or, I could be mis-interpreting what I should expect to get from the tls_as_xyz procedure. I'd be happy to share details off-line with any one who might volunteer to help. ...thanks...dave case

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