- phenixbb - phenix-online.org

phenix.polder - tool for calculating omit maps by excluding bulk solvent
by Dorothee Liebschner 22 Apr '16

22 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 22 Apr '16

22 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 21 Apr '16

21 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 21 Apr '16

21 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 21 Apr '16

21 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 21 Apr '16

21 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 19 Apr '16

19 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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Application deadline is this week: CCP4/APS crystallographic school, June 21 - 29, 2016
by Sanishvili, Ruslan 19 Apr '16

19 Apr '16

Dear Colleagues, Deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. If you have a crystallographic problem you cannot resolve independently, this school is for you. From our past experience, the majority of participants bring with them the crystallographic problems and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed at http://www.ccp4.ac.uk/schools/APS-school/publications.php This school will cover popular packages such as CCP4, PHENIX, SHELX and much, much more: http://www.ccp4.ac.uk/schools/APS-2016/program.php Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found at: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Wednesday, March 23, 2016 10:26 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] Reminder, CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, This is a reminder that the application deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. The school will take place from June 21 through June 29, 2016 at the Advanced Photon Source, Argonne National Laboratory, near Chicago. All aspects of macromolecular crystallography from data collection to structure refinement and validation, as well as functional assessment, will be covered. Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. >From our past experience, the majority of participants bring with them the crystallographic problems they cannot resolve independently and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed here: http://www.ccp4.ac.uk/schools/APS-school/publications.php Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found here: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Tuesday, February 23, 2016 7:48 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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Re: [phenixbb] Data processing: exhaustive search?
by Kay Diederichs 17 Apr '16

17 Apr '16

Hi Kaushik, there is no need for, and no sense in, an exhaustive search of data processing parameter space, because its dimensionality is way too high to achieve anything useful. The programs MOSFLM and XDS have undergone decades of development, and their processing defaults are carefully chosen. It is rather the user of the programs who is in charge to correctly interpret the output (which requires reading of their documentation, and some experience), and to make meaningful adjustments to (usually very) few parameters. Speaking for XDS, I recommend to read XDSwiki articles (there are tutorials and example data sets, and lots of explanations) and a book chapter that I recently wrote (#131 at http://cms.uni-konstanz.de/strucbio/diederichs-group/publications ). If you use the generate_XDS.INP script from XDSwiki, and follow the paper and the "Optimization" article, you will get good data from XDS. (There are other scripts, like autoPROC, xia2, xdsme and so on, which usually also give good results but I don't know them well.) In particular, in case of XDS there is usually no need to fiddle around with "box size, spot separation, tolerance and other parameters". The fact that you seem to try and optimize Rmerge suggests to me that you are trading precision for accuracy. Too many people still do this, but it is a legacy of the past. "Trying a combination of better frames over poorer frames" is most likely _not_ going to improve your merged intensities - this is another unfortunate and very common misunderstanding (see references 113 and 130). I hope this helps you to get better data. Kay On 16.04.2016 21:18, phenixbb-request(a)phenix-online.org wrote: > Message: 6 > Date: Sun, 17 Apr 2016 00:48:31 +0530 > From: Kaushik Hatti <hskaushik(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Data processing: exhaustive search? > Message-ID: > <CAGMFGb=B9s-j4yXmRx8_M7NPndf86puviiY9QMg=EAqaWr9thw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I have a data set diffracted to 2.7A collected at 1.54 wavelength. The data > is not of great quality with very close spots, ellipsoid spots in certain > regions of the frames and spot overlaps. Also certain frames are poorer > than rest. The crystal could not be reproduced. > > The best R merge (overall) I have achieved so far is 17% with 85% > completeness and 3 I/SigI processed in P4 space group. I feel it's possible > to process it better by identifying right values for box size, spot > separation, tolerance and other parameters. I am also suspecting a higher > symmetry space group. I believe, trying a combination of better frames > over poorer ones with improve merging statistics. > > I have so far tried processing in iMosflm and XDS. Is there a tool which > could search exhaustively trying different values for parameters and > suggest the combination which provide best merging statistics? > > Sorry if this question is not relevant in this group. > Any pointers/suggestions would be gratefully helpful. > > Thanks in advance, > Regards, > Kaushik > Molecular Biophysics Unit, > Indian Institute of Science, > Bangalore, India. -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz

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