- phenixbb - phenix-online.org

Phenix version 1.14 released
by Paul Adams 25 Sep '18

25 Sep '18

The Phenix developers are pleased to announce that version 1.14 of Phenix is now available (build 1.14-3260). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for this version: - Reorganization, updates and addition of cryo-EM tools: - phenix.mtriage - assess map and model quality - phenix.auto_sharpen - map sharpening - phenix.map_symmetry - identify symmetry in maps - phenix.map_box - cut out unique parts of maps - phenix.combine_focused_maps - combine different maps - phenix.dock_in_map - automatically place an atomic model into a map - phenix.map_to_model - automatically build atomic model from a map - phenix.sequence_from_map - identify sequence from a map - phenix.real_space_refine - improved refinement of models - phenix.validation_cryoem - separate tool for comprehensive validation of models and maps - phenix.cablam_idealization - Tool to automatically fix Cablam outliers - eLBOW - better support for metals and metal clusters - added plugin for QM package Orca - Phaser-2.8.2 - bugfixes - Phassade substructure search when starting from seed substructure - fix crash in MR_ATOM - problems with cumulative intensity distribution for extremely weak data - improve computation and presentation of data information content - Performance improvements - NCS search - Generation of secondary structure restraints - Clashscore calculation - AmberPrep is more robust - Restraints for ARG improved - New Phenix video tutorials - GUI - New section in main window for cryo-EM tools - Separate validation GUI for cryo-EM structures - Added phenix.map_symmetry - Added phenix.dock_in_map - Added phenix.map_to_structure_factors - Added phenix.combine_focused_maps - Added phenix.sequence_from_map - phenix.ligand_identification: - Added an option to generate ligand library based on sequence and structural homologs of the input pdb model. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). 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. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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TER card only at the end of polymer chains of pdb file
by Maxime Cuypers 25 Sep '18

25 Sep '18

Hello, The pdb deposition server only allows deposition of pdb files that have a TER card at the end of polymer chains. But phenix add a ter card at the end of each chain, regardless of the content or whether or not the TER card was present before refinement or not. Would it be possible to have this automagically handled by phenix.refine so the user does not encur the frustrating systematic error during deposition and need to edit the pdb file every time a 'final refinement' is tested for validation ? does that make sense? cheerios to all, Maxime

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Fw: AsCA 2018 / CRYSTAL 32: Early bird Closing
by Christopher Squire 24 Sep '18

24 Sep '18

?? [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] Dear Colleagues, Early bird closing 2 October 2018 A friendly reminder that early bird rates to attend the AsCA 2018/CRYSTAL 32 conference will finish on 2 October 2018. Register today using (http://asca2018.org/registration/) to secure the discounted rate. The conference will run from 2-5 December 2018. Keep up-to-date with our conference programme<http://asca2018.org/programme/>, outstanding lineup of workshops<http://asca2018.org/workshops/>, and speakers<http://asca2018.org/speakers/>. Don't forget to get in early and book your accommodation<http://asca2018.org/accommodation/> too! We look forward to meeting you in Auckland. Kind regards, Dr. Christopher Squire (University of Auckland), Professor Ted Baker (University of Auckland), Professor Kurt Krause (University of Otago) and the AsCA 2018/CRYSTAL 32 Committee http://asca2018.org/ [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…]

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Rfree set with twin refinement
by Matthew Bick 23 Sep '18

23 Sep '18

Hello PhenixBB I am dealing with a structure that is twinned and would like to ensure that the Rfree set I'm using is unbiased. This is what I have done so far. - Generated an initial model after Phaser MR using Autobuild. The input "Experimental Data" for autobuild was an XDS_ASCII.hkl file from data processed with XDS (along with the phaser output mtz as the "initial map"). Autobuild generates the file "exptl_fobs_phases_freeR_flags.mtz" containing the Rfree set, which I have used for all subsequent rounds of Phenix.refine. - I have built the model to completion with Coot and Phenix.refine, without applying the twin law. Only at the final round of refinement did I apply twin refinement, and it is obvious that the data is twinned (Xtriage also suggests twinning). My question - when the Rfree is established during Autobuild, does Phenix take into account all of the possible twin laws, so that the free and working sets are not related in any way by the possible twin laws? I believe Phenix does do this, but I would like to make sure. Space group is P 1 21 1 and the twin law is pseudo-merohedral h,-k,-h-l, in case those are relevant. Thank you. Matthew Bick

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Recruiting fragment/XChem crystallographers
by Frank von Delft 21 Sep '18

21 Sep '18

Hi all - We have vacancies at SGC (in my and Prof. Paul Brennan's groups) for crystallographers interested in driving a series of new genetically validated targets (inflammation and Alzheimers) from gene to XChem fragment screening and beyond to potency, and helping figure out how to do all of this a lot better than we currently can. Link is here <https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.disp…>, and deadline is in two weeks (October 5th). Frank -- Prof Frank von Delft Associate Professor Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F) Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile)

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Secondary structure restraints video tutorial
by Dorothee Liebschner 14 Sep '18

14 Sep '18

Dear Phenix users, This is an update for the Phenix video tutorials. We have a new tutorial explaining the use of secondary_structure_restraints <https://www.phenix-online.org/documentation/reference/secondary_structure.h…>, a type of restraints especially useful at low resolution (lower than 3Å, cryo-EM map or X-ray data). References: Programming new geometry restraints: parallelity of atomic groups. Sobolev OV et al. J. Appl. Cryst. 48, 1130-1141 (2015). https://doi.org/10.1107/S1600576715010432 Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Headd JJ et al. Acta Cryst. D68, 381-390 (2012). https://doi.org/10.1107/S0907444911047834 Feedback about the videos is very welcome. Write an email to tutorials @phenix-online.org or use the comment section on YouTube. If you want to see a tutorial about a certain (Phenix-related) topic, let us know. Best wishes, The Phenix team ------------------------------- Overview of tutorials: https://www.phenix-online.org/documentation/reference/tutorial_channel.html You can also browse the videos on the Phenix Tutorial YouTube channel: https://www.youtube.com/c/phenixtutorials (To see subtitles, hit the cc (closed captions) button in the right bottom of the video screen. Subscribe to see the tutorial videos in your YouTube subscription feed. To get notifications about new videos, tap the bell button, which is next to the "subscribe" button.)

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submission of neutron structure containing "H" atoms on the pdb database problematic
by Maxime Cuypers 11 Sep '18

11 Sep '18

Dear all, i was wondering if others have encountered the same problems with the PDB database curation rules or if this is a first. I am trying to submit a neutron structure with 'free' H atoms (protons) clearly identified. (not D atoms here), this is a situation similar to how D atoms can be reported in a pdb neutron structure close to a carboxylic residue or other situation like in the D‐xylose isomerase (XI). I have first tried to submit the neutron structure with the H atoms part of the complex molecules nearby but i faced refusal and was asked to make it as simple 'H' atoms. once i had done the 'free' H atoms version of the pdb, the structure was again refused by curators because there is no library available to the pdb curators to accept such H atoms. I was explained that it had been decided to ban the 'H' atom only coordinate from depositions some years ago. What would you recommand me to do to get the structure deposited and curated keeping the valid coordinates of the H atoms in the pdb file? PS: this is not fantasy. Dr. Maxime Cuypers

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single atom mmcif bug
by Edwin Pozharski 05 Sep '18

05 Sep '18

There appears to be a bug in phenix.cif_as_pdb. I am looking at a bunch of files that contain very few atoms. When it's more than one, mmcif contains multiple HETATM records in a loop. However, single atom entries seem to encode atomic coordinates in a different way, like so # _atom_site.group_PDB HETATM _atom_site.id 4905 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_alt_id . _atom_site.label_comp_id CA _atom_site.label_asym_id L _atom_site.label_entity_id 5 _atom_site.label_seq_id . _atom_site.pdbx_PDB_ins_code . _atom_site.Cartn_x 0.394 _atom_site.Cartn_y -6.965 _atom_site.Cartn_z 18.775 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 2 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_asym_id A _atom_site.auth_seq_id 701 _atom_site.pdbx_PDB_model_num 1 This does not include _loop statement and instead lists parameters directly. If I try to convert this to pdb, cif_as_pdb fails like so (and I suspect that pretty much any cif-file read would fail) Python argument types in double.__init__(double, str) did not match C++ signature: __init__(boost::python::api::object, boost::python::numeric::array) __init__(boost::python::api::object, boost::python::tuple) __init__(boost::python::api::object, boost::python::list) __init__(boost::python::api::object, std::vector<double, std::allocator<double> >) __init__(boost::python::api::object, scitbx::af::const_ref<std::string, scitbx::af::trivial_accessor>) __init__(_object*, scitbx::af::shared_plain<double>) __init__(_object*, unsigned long) __init__(_object*, unsigned long, double) __init__(_object*, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> >) __init__(_object*, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> >, double) __init__(_object*) This has nothing to do with how many atoms are there, obviously - in fact, removing all HETATM records but one from a cif file that has _loop statement does not produce this bug. The obvious guess is that the bug is somewhere in mmdb (I am assuming here that phenix relies on it for cif read/write). This is not a big deal, of course - in most scenarios, a structure contains more than one atom. It does not interfere with me either - I am discarding single atom cases in this analysis anyway (so it is actually serves as an unintentional filter). Still, it looks like a bug. I am not an expert in mmcif format, but iiuc, there is no strict requirement for atom_site category to have a _loop. If there is (I can't find any such syntax requirement), then the source of the data files (PDBe coordinate server) would be at fault for not structuring the data properly. Cheers, Ed.

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Charged Ammonium ligand exploding
by pramod kumar 04 Sep '18

04 Sep '18

Dear All, I have a protein-ligand complex cryo-EM data. The ligand is a primary amine, which at the neutral pH used during data collection, should be NH3+ (alkyl-amonium). However, during realspace refine and despite having provided the CIF file (elbow generated alkyl-ammonium form), the molecule keeps "exploding". Instead, the 'NH2 form' (alkyl-amine) remains stable during refinement and most of the pdb entries having alkylammonium molecules have modeled them as the amine form even when they are expected to be positively charged. Thus, it seems to me that other groups may have gone through the same difficulties when trying to refine ammonium groups. We have already tried: * Ligand build in Lidia and tried prodrg with error (*Unrecognised REFMAC atom type 'HCH3' in input*) * Refmac Acedrg (run201 Error in wrapper refmac) Please help me fix this. I could refine using the amine form, but I know that the amine form is not right. Thank you very much, in advance. -- Promod Jaykar, Ph.D.

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autosol: FATAL RUNTIME ERROR :Wavelength outside range of Sasaki tables.
by Georg Mlynek 27 Aug '18

27 Aug '18

Dear Phaser Developers, we have collected data at diamond at 3A wavelength for Ca-MAD. Running autosol supplying the peak and remote dataset I get a solution. However the resolution is too low for autobuild to be successful. Therefore I continued with MR-SAD supplying the peak data=overall_best_refine_data.mtz This is my input mtz However get this error message: Error message from Phaser: FATAL RUNTIME ERROR :Wavelength outside range of Sasaki tables. Use SCATTERING to specify f' and f" for atom(s) "S" Phaser phasing did not work Scattering factors for Ca will be f'= -6.74 f''= 6.55 Using partial model pdb file as substructure: /home/g/r/aactn1_merge/phaser_31/aactn1_merge_phaser.1.pdb with RMS= 0.7 Data output to : AutoSol_run_32_/TEMP0/phaser_mtz FATAL RUNTIME ERROR :Wavelength outside range of Sasaki tables. Use SCATTERING to specify f' and f" for atom(s) "S" Phaser phasing did not work Analysis failed on solution evaluation *If I specify S as atom it continues without any problem however I get this warning, which I don't understand scientifically.* The same error I get (of course) when I would like to run PHASER-EP I guess the errors are just resulting from the programs not adjusted to the longwavelength beamline. Many thanks, best regards Georg.

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AsCA 2018: Submission Deadline Next Week!
by Christopher Squire 24 Aug '18

24 Aug '18

[https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] Dear Colleagues, Abstract and Awards & Scholarships Submission Deadlines Approaching Do not forget to submit your abstract for oral presentations before 1 September 2018! Visit the AsCA 2018/CRYSTAL 32 conference website at http://asca2018.org/call-for-abstracts/ for guidelines, and submission details. In addition to oral presentations, we also welcome poster presentations. The deadline for poster submissions is 1 November 2018. The deadline for awards and travel scholarships is also closing on 1 September. Check out the details online<http://asca2018.org/awards/> and download the application form. If you're planning on coming along to the conference, be sure to register using your before 2 October 2018 to ensure you take advantage our our discounted early-bird rates. Please register online at http://asca2018.org/registration/. The conference will run from 2-5 December 2018. Keep up-to-date with our conference programme<http://asca2018.org/programme/>, outstanding lineup of workshops<http://asca2018.org/workshops/>, and speakers<http://asca2018.org/speakers/>. Don't forget to get in early and book your accommodation<http://asca2018.org/accommodation/> too! Important Dates: 1 September 11.59pm NZST - Submission deadline for those requesting oral presentations 1 September - Submission deadline for awards and travel scholarships 2 October - Early-bird registration closes 1 November - Submission deadline for those requesting poster presentations 2-5 December - Conference We look forward to meeting you in Auckland. Kind regards, Dr. Christopher Squire (University of Auckland), Professor Ted Baker (University of Auckland), Professor Kurt Krause (University of Otago) and the AsCA 2018/CRYSTAL 32 Committee. [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…]

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Rosetta refinement fail on Mac
by Aaron Oakley 22 Aug '18

22 Aug '18

System: macOS 10.13.6 Phenix version: phenix-1.14rc1-3177 Rosetta version: 3.9 (rosetta_src_2018.09.60072_bundle) So I rebuilt rosetta 3.9 as root and can now run "Rosetta refinement". However...Rosetta refinement ran for 2 hours, slowly gobbling memory up to a maximum of 25GB before failing (error below). Also gobbled up disk space, creating a 78 GB file “outtmp.map”. A memory leak issue? Thanks, a++ RuntimeError : File 'None' not found. Traceback: File "/Applications/phenix-1.14rc1-3177/modules/cctbx_project/libtbx/runtime_utils.py", line 179, in run return_value = self.target() File "/Applications/phenix-1.14rc1-3177/modules/cctbx_project/libtbx/runtime_utils.py", line 74, in __call__ result = self.run() File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/command_line/rosetta_refine.py", line 304, in run return run(args=list(self.args)) File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs check_result(result) File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 383, in check_result raise RuntimeError("File '%s' not found." % result.file_name)

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Fwd: Off topic: Announcing the 76th Annual Pittsburgh Diffraction Conference October 14th – 16th Case Western Reserve University, Cleveland, OH
by John Rose 22 Aug '18

22 Aug '18

Hi, For those of you who may be interested. Regards, John Announcing the 76th Annual Pittsburgh Diffraction Conference October 14th – 16th Case Western Reserve University, Cleveland, OH Dear Colleague: On behalf of the program committee, you and your colleagues are cordially invited to join us for the 76th Annual Pittsburgh Diffraction Conference at Case Western Reserve University. Biomolecular topics include: X-ray Crystallography Cryo-EM X-ray tomography Cryo -ET X-ray free electron lasers Students welcome - prizes awarded for the top posters Please submit abstracts to pxk258(a)case.edu <mailto:[email protected]> (Deadline September 14, 2018) Venue Iris S. & Bert L. Wolstein Research Building, Case Western Reserve University, Cleveland, OH Conference Registration (Deadline August 27, 2018) To insure maximum participation, the cost of attending the conference has been kept to a minimum ($80.00 for professionals, $25.00 graduate students). Registration Link - https://goo.gl/forms/oSfoXVNgSTDqOEPC3 <https://goo.gl/forms/oSfoXVNgSTDqOEPC3> Conference Accommodations (Deadline September 14, 2018) A block of rooms has been reserved at the Cleveland Courtyard Marriott - 2021 Cornell Road, Cleveland Ohio 44106 (1(216) 791-567 and mention the e Pittsburgh Diffraction Conference for a discounted rate). Accommodations Link https://www.marriott.com/hotels/travel/clece-courtyard-cleveland-university… <https://www.marriott.com/hotels/travel/clece-courtyard-cleveland-university…> Poster Session and Social Events Poster sessions and social events, included in the program, provide many opportunities for formal and informal discussions with the speakers. The Chung Soo Yoo Award will be given to graduate students for best poster presentation. Program Organizers - Edward Yu and Tsan Sam Xiao For more information - Please contact Edward Yu (ewy5(a)case.edu <mailto:[email protected]>) We look forward to seeing you in Cleveland! John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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install Rosetta for use in Phenix fails
by Aaron Oakley 21 Aug '18

21 Aug '18

I have repeatedly tried to install Rosetta for use in Phenix with zero success. System: macOS 10.13.6 Phenix version: phenix-1.14rc1-3177 Rosetta version: 3.9 (rosetta_src_2018.09.60072_bundle) Relevant environmental variables: ROSETTA3_DB=/usr/local/rosetta_src_2018.09.60072_bundle/main/database ROSETTA_TOOLS=/usr/local/rosetta_src_2018.09.60072_bundle/tools ROSETTA3=/usr/local/rosetta_src_2018.09.60072_bundle/main/source PHENIX=/Applications/phenix-1.14rc1-3177 PHENIX_VERSION=1.14rc1-3177 PHENIX_ROSETTA_PATH=/usr/local/rosetta_src_2018.09.60072_bundle rosetta.build_phenix_interface —seemed— to work OK. However... rosetta.run_tests fails with DEBUG dumping error message ERROR: Rosetta exited with status 1 stderr output: BACKTRACE: 0 libcore.3.dylib 0x0000000114b0e4e6 print_backtrace(char const*) + 54 …40 lines of traceback crap… Traceback (most recent call last): File "/Applications/phenix-1.14rc1-3177/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 307, in <module> run(sys.argv[1:], create_dir=True) File "/Applications/phenix-1.14rc1-3177/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs check_result(result) File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Any ideas? Aaron Oakley

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rosetta installation problem ubuntu 18.04
by Georg Mlynek 20 Aug '18

20 Aug '18

Dear Scientific Community, I am struggling installing rosetta on ubuntu 18.04.1 LTS and phenix 1.14-3211-000. I followed the instruction as in https://www.phenix-online.org/documentation/reference/rosetta_install.html the provided link https://c4c.uwc4c.com/express_license_technologies/rosetta gives an "This site can't be reached error" Therfore I went to https://www.rosettacommons.org/software and downloaded and unpacked in /home/g/programs/rosetta_src_2016.32.58837_bundle/ I added the line export PHENIX_ROSETTA_PATH=/home/g/programs/rosetta_src_2016.32.58837_bundle/ to .bashrc running rosetta.build_phenix_interface nproc=8 I can't remember if it was fine. Running it now gives g@glap:~$ rosetta.build_phenix_interface nproc=8 Substituting phenix.python into build shell scripts update_options.sh update_ResidueType_enum_files.sh Applying patch patching file source/src/core/kinematics/tree/Atom.hh Reversed (or previously applied) patch detected! Assume -R? [n] *pressing n* Apply anyway? [n] n Skipping patch. 2 out of 2 hunks ignored -- saving rejects to file source/src/core/kinematics/tree/Atom.hh.rej patching file source/src/core/kinematics/tree/Atom_.cc Hunk #1 FAILED at 817. 1 out of 1 hunk FAILED -- saving rejects to file source/src/core/kinematics/tree/Atom_.cc.rej patching file source/src/core/kinematics/tree/Atom_.hh Hunk #1 FAILED at 467. 1 out of 1 hunk FAILED -- saving rejects to file source/src/core/kinematics/tree/Atom_.hh.rej patching file source/src/core/kinematics/tree/BondedAtom.cc Hunk #1 FAILED at 542. 1 out of 1 hunk FAILED -- saving rejects to file source/src/core/kinematics/tree/BondedAtom.cc.rej patching file source/src/core/kinematics/tree/BondedAtom.hh Hunk #1 FAILED at 259. 1 out of 1 hunk FAILED -- saving rejects to file source/src/core/kinematics/tree/BondedAtom.hh.rej patch unexpectedly ends in middle of line Phenix modules found : /usr/local/phenix-1.14-3211/modules/phenix Traceback (most recent call last): File "/usr/local/phenix-1.14-3211/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 265, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.14-3211/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 225, in run f=file("dispatcher_include_erraser.sh", "wb") IOError: [Errno 13] Permission denied: 'dispatcher_include_erraser.sh' *running the run test gives following.* lap:~$ rosetta.run_tests Running Rosetta refinement tests /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.pdb /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz phenix.rosetta_refine /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.pdb /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz number_of_models=2 ============================== Collecting inputs ============================== ----------Processing X-ray data---------- F-obs: /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X Miller array info: /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X Observation type: xray.amplitude Type of data: double, size=495 Type of sigmas: double, size=495 Number of Miller indices: 495 Anomalous flag: False Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 199 Resolution range: 22.4416 1.80066 Completeness in resolution range: 0.895118 Completeness with d_max=infinity: 0.895118 Wavelength: 1.0000 Number of F-obs in resolution range: 495 Number of F-obs<0 (these reflections will be rejected): 0 Number of F-obs=0 (these reflections will be used in refinement): 0 Refinement resolution range: d_max = 22.4416 d_min = 1.8007 R-free flags: /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags Miller array info: /usr/local/phenix-1.14-3211/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags Observation type: None Type of data: int, size=495 Type of sigmas: None Number of Miller indices: 495 Anomalous flag: False Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 199 Resolution range: 22.4416 1.80066 Completeness in resolution range: 0.895118 Completeness with d_max=infinity: 0.895118 Wavelength: 1.0000 Test (R-free flags) flag value: 1 Number of work/free reflections by resolution: work free %free bin 1: 22.4433 - 3.8734 [61/70] 59 2 3.3% bin 2: 3.8734 - 3.0770 [53/58] 49 4 7.5% bin 3: 3.0770 - 2.6887 [49/55] 46 3 6.1% bin 4: 2.6887 - 2.4432 [37/40] 35 2 5.4% bin 5: 2.4432 - 2.2683 [62/66] 60 2 3.2% bin 6: 2.2683 - 2.1347 [51/56] 49 2 3.9% bin 7: 2.1347 - 2.0278 [50/55] 46 4 8.0% bin 8: 2.0278 - 1.9396 [49/56] 49 0 0.0% bin 9: 1.9396 - 1.8650 [43/50] 42 1 2.3% bin 10: 1.8650 - 1.8007 [40/47] 40 0 0.0% overall 475 20 4.0% ----------Processing PDB file(s)---------- Monomer Library directory: "/usr/local/phenix-1.14-3211/modules/chem_data/mon_lib" Total number of atoms: 66 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: " " Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 0.13, per 1000 atoms: 1.97 Number of scatterers: 66 At special positions: 0 Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90) Space group: P 1 21 1 (No. 4) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 21 8.00 N 12 7.00 C 33 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of custom bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of custom angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: atom_selection = None None Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : False - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.02 Conformation dependent library (CDL) restraints added in 3.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 12 Time building geometry restraints manager: 0.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 13 1.29 - 1.36: 11 1.36 - 1.42: 7 1.42 - 1.49: 6 1.49 - 1.55: 22 Bond restraints: 59 Sorted by residual: bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.507 -0.056 1.60e-02 3.91e+03 1.23e+01 bond pdb=" CA GLN A 4 " pdb=" C GLN A 4 " ideal model delta sigma weight residual 1.522 1.553 -0.030 1.18e-02 7.18e+03 6.53e+00 bond pdb=" N GLN A 4 " pdb=" CA GLN A 4 " ideal model delta sigma weight residual 1.460 1.485 -0.025 1.17e-02 7.31e+03 4.40e+00 bond pdb=" CA ASN A 2 " pdb=" C ASN A 2 " ideal model delta sigma weight residual 1.524 1.498 0.025 1.26e-02 6.30e+03 4.00e+00 bond pdb=" CA ASN A 6 " pdb=" C ASN A 6 " ideal model delta sigma weight residual 1.526 1.504 0.022 1.28e-02 6.10e+03 2.85e+00 ... (remaining 54 not shown) Histogram of bond angle deviations from ideal: 107.05 - 110.59: 8 110.59 - 114.13: 19 114.13 - 117.67: 11 117.67 - 121.21: 23 121.21 - 124.75: 18 Bond angle restraints: 79 Sorted by residual: angle pdb=" N ASN A 3 " pdb=" CA ASN A 3 " pdb=" C ASN A 3 " ideal model delta sigma weight residual 108.90 113.48 -4.58 1.63e+00 3.76e-01 7.90e+00 angle pdb=" N GLN A 4 " pdb=" CA GLN A 4 " pdb=" C GLN A 4 " ideal model delta sigma weight residual 108.02 111.93 -3.91 1.78e+00 3.16e-01 4.84e+00 angle pdb=" CA GLN A 4 " pdb=" C GLN A 4 " pdb=" O GLN A 4 " ideal model delta sigma weight residual 120.33 122.27 -1.94 1.08e+00 8.57e-01 3.23e+00 angle pdb=" CA GLN A 5 " pdb=" C GLN A 5 " pdb=" O GLN A 5 " ideal model delta sigma weight residual 120.38 122.31 -1.93 1.09e+00 8.42e-01 3.13e+00 angle pdb=" C GLN A 4 " pdb=" N GLN A 5 " pdb=" CA GLN A 5 " ideal model delta sigma weight residual 123.00 120.57 2.43 1.38e+00 5.25e-01 3.09e+00 ... (remaining 74 not shown) Histogram of dihedral angle deviations from ideal: 0.04 - 14.51: 26 14.51 - 28.98: 5 28.98 - 43.45: 1 43.45 - 57.92: 1 57.92 - 72.39: 1 Dihedral angle restraints: 34 sinusoidal: 15 harmonic: 19 Sorted by residual: dihedral pdb=" CA ASN A 3 " pdb=" C ASN A 3 " pdb=" N GLN A 4 " pdb=" CA GLN A 4 " ideal model delta harmonic sigma weight residual 180.00 166.21 13.79 0 5.00e+00 4.00e-02 7.60e+00 dihedral pdb=" CB GLN A 5 " pdb=" CG GLN A 5 " pdb=" CD GLN A 5 " pdb=" OE1 GLN A 5 " ideal model delta sinusoidal sigma weight residual 0.00 -72.39 72.39 2 3.00e+01 1.11e-03 4.85e+00 dihedral pdb=" CB GLN A 4 " pdb=" CG GLN A 4 " pdb=" CD GLN A 4 " pdb=" OE1 GLN A 4 " ideal model delta sinusoidal sigma weight residual 0.00 54.08 -54.08 2 3.00e+01 1.11e-03 3.50e+00 ... (remaining 31 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1 0.024 - 0.047: 1 0.047 - 0.071: 1 0.071 - 0.094: 1 0.094 - 0.118: 2 Chirality restraints: 6 Sorted by residual: chirality pdb=" CA GLN A 5 " pdb=" N GLN A 5 " pdb=" C GLN A 5 " pdb=" CB GLN A 5 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ASN A 6 " pdb=" N ASN A 6 " pdb=" C ASN A 6 " pdb=" CB ASN A 6 " both_signs ideal model delta sigma weight residual False 2.51 2.62 -0.11 2.00e-01 2.50e+01 2.86e-01 chirality pdb=" CA ASN A 2 " pdb=" N ASN A 2 " pdb=" C ASN A 2 " pdb=" CB ASN A 2 " both_signs ideal model delta sigma weight residual False 2.51 2.43 0.08 2.00e-01 2.50e+01 1.80e-01 ... (remaining 3 not shown) Planarity restraints: 13 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 7 " -0.006 2.00e-02 2.50e+03 9.66e-03 1.87e+00 pdb=" CG TYR A 7 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 7 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 7 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 7 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 7 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 7 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 7 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 2 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" CG ASN A 2 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 2 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 2 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 4 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00 pdb=" C GLN A 4 " -0.019 2.00e-02 2.50e+03 pdb=" O GLN A 4 " 0.007 2.00e-02 2.50e+03 pdb=" N GLN A 5 " 0.006 2.00e-02 2.50e+03 ... (remaining 10 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 50 3.00 - 3.48: 107 3.48 - 3.95: 243 3.95 - 4.42: 255 4.42 - 4.90: 523 Nonbonded interactions: 1178 Sorted by model distance: nonbonded pdb=" OH TYR A 7 " pdb=" O HOH 11 " model vdw sym.op. 2.525 2.440 -x+1,y-1/2,-z+1 nonbonded pdb=" O HOH 11 " pdb=" OH TYR A 7 " model vdw sym.op. 2.525 2.440 -x+1,y+1/2,-z+1 nonbonded pdb=" O HOH 14 " pdb=" O HOH 13 " model vdw sym.op. 2.634 2.440 x,y-1,z nonbonded pdb=" O HOH 13 " pdb=" O HOH 14 " model vdw sym.op. 2.634 2.440 x,y+1,z nonbonded pdb=" N GLY A 1 " pdb=" O GLY A 1 " model vdw 2.665 2.496 ... (remaining 1173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 3 Type Number sf(0) Gaussians O 21 7.97 2 N 12 6.97 2 C 33 5.97 2 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 66 At special positions: 0 Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90) Space group: P 1 21 1 (No. 4) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.: 495 re-set all scales: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.: 495 remove outliers: r(all,work,free)=0.2103 0.2117 0.1924 n_refl.: 493 bulk-solvent and scaling: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.: 493 remove outliers: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.: 493 |--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06 % free)--------------| | | | r_work= 0.1758 r_free= 0.1728 coordinate error (max.-lik. estimate): -0.00 A| | | | normalized target function (ml) (work): 2.637727 | | target function (ml) not normalized (work): 1247.644901 | | target function (ml) not normalized (free): 60.766973 | |-----------------------------------------------------------------------------| End of input processing Sorry: The RosettaScripts executable could not be located. Please set the environmental variable PHENIX_ROSETTA_PATH or add the appropriate directory to your PATH environment variable. *I am grateful for any advice.* *Best regards, Georg.*

2 1

RSCC calculation for structures from ensemble refinement
by Ashraya Ravikumar 20 Aug '18

20 Aug '18

Hi, I performed ensemble refinement for an existing PDB structure using phenix.ensemble_refinement. May I know what is the best way to calculate real space correlation coefficient at the residue level for the ensemble? I tried using phenix.real_space_correlation but it gave me the following error: "Sorry: Multiple equally suitable arrays of observed xray data found." Thanks in advance. Regards, Ashraya Ravikumar, Graduate Student, Indian Institute of Science

1 0

Re: [phenixbb] Questions about refine glycans using PHENIX
by Nigel Moriarty 08 Aug '18

08 Aug '18

Miao The glycans should be automatically linked and listed in the log file. You can do a quick check there. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Aug 8, 2018 at 2:28 AM Miao Gui <gmhust2007(a)163.com> wrote: > Dear Pavel, > > Thank you very much for your reply. > Actually, the models as well as the glycans look quite good after PHENIX > real-space refinement. I just want to make sure that this is the right way > since it's my first time to refine a glycan. > > Hope to see you in Tsinghua! > > Best wishes, > > Miao > > > > > > At 2018-08-08 00:46:37, "Pavel Afonine" <pafonine(a)lbl.gov> wrote: > > Hi, > > yes, as long as the map shows the glycans clearly enough so that you can > model them, then there is no problem refining your model using > phenix.real_space_refine. Normally, there is no need to add anything > special. > Now I'm puzzled.. do you have a reason to believe that something isn't > working correctly? > > By the way, we will be at Tsinghua University first week of September > running Phenix workshop. We can discuss things while there! > > All the best, > Pavel > > On 8/7/18 08:16, Miao Gui wrote: > > Dear phenix developers, > > I'm a PHENIX user. PHENIX helped me a lot when refining structural models > against cryo-EM maps. > > Recently, I built a structural model of a glycoprotein and added the > glycans using COOT against a 3.4 A cryo-EM map. Then I want to refine the > model using PHENIX.real_space_refine. I always add the second structure > restrains when refining the models against cryo-EM maps. Do I need to add > other restrains for the glycans? Is it appropriate to refine the > glycoprotein using the real_space_refine? > Thank you. > > Best wishes, > > Dr. Miao Gui > Tsinghua University, Beijing > > > > > > > > >

1 0

Re: [phenixbb] Questions about refine glycans using PHENIX
by Pavel Afonine 07 Aug '18

07 Aug '18

Hi, yes, as long as the map shows the glycans clearly enough so that you can model them, then there is no problem refining your model using phenix.real_space_refine. Normally, there is no need to add anything special. Now I'm puzzled.. do you have a reason to believe that something isn't working correctly? By the way, we will be at Tsinghua University first week of September running Phenix workshop. We can discuss things while there! All the best, Pavel On 8/7/18 08:16, Miao Gui wrote: > Dear phenix developers, > > I'm a PHENIX user. PHENIX helped me a lot when refining structural > models against cryo-EM maps. > > Recently, I built a structural model of a glycoprotein and added the > glycans using COOT against a 3.4 A cryo-EM map. Then I want to refine > the model using PHENIX.real_space_refine. I always add the second > structure restrains when refining the models against cryo-EM maps. Do > I need to add other restrains for the glycans? Is it appropriate to > refine the glycoprotein using the real_space_refine? > Thank you. > > Best wishes, > > Dr. Miao Gui > Tsinghua University, Beijing > >

1 0

Post Doctoral Research Fellow opportunity - Structural Chemistry Group at MD Anderson Cancer Center's Therapeutics Division.
by Leonard,Paul G 03 Aug '18

03 Aug '18

At MD Anderson, we have been working to eliminate cancer for more than seven decades and are ranked as one of the top two hospitals in cancer care every year since 1990. One of our greatest strengths is our ability to translate today's most promising laboratory findings into tomorrow's new, more effective and less traumatic treatments. We are recruiting exceptional national and international post-doctoral fellowsto join our Structural Chemistry group, part of the Institute for Applied Cancer Science. Applicants must be extremely motivated and possess a strong background in structural biology, including protein expression and purification, crystallization, and X-ray crystallography. Experience using other biophysical techniques would be an advantage. We are seeking only the most dedicated individuals who will join us in our quest to discover, develop, and deliver more effective treatments to our patients. This is a unique opportunity to participate in project-driven drug discovery research within a highly respected academic and clinical setting. We’re tackling cancer and neurodegeneration with a new plan — our Moon Shots Program - one that aims to improve prevention, early detection and treatment. Our research engines fuel innovation along the way. And innovation, collaboration and scale get us there faster. They give us the framework we need for success, and speed up development for new and more effective care. Our Missionis to integrate novel biological insights with drug discovery expertise to accelerate the development of innovative targeted therapeutics, both small molecules and biologics for unmet medical needs. Our work is conducted in an environment that brings together excellence in both academic and pharmaceutical discovery, as evidenced by recent publications. Visit our platforms at https://www.mdanderson.org/cancermoonshots.html Interested individuals should send a cover letter describing their research experience, and a curriculum vitae, to: MD Anderson Therapeutics Division (therapeutics(a)mdanderson.org<mailto:[email protected]>) The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

1 0

Fw: AsCA 2018 Programme Announcement
by Christopher Squire 02 Aug '18

02 Aug '18

?[https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-public/d231daa0bdac4db99817bc87d65a4b98] Dear Colleagues, The full agenda for the AsCA 2018/CRYSTAL 32 Conference<http://asca2018.org/programme/> is now available online. We invite you to explore our programme of oral presentations, poster presentations, and workshops, displaying outstanding science from Asia, Australia and New Zealand, and from around the world. If you haven't already, register today<http://asca2018.org/registration/> at the early-bird rate to connect with the scientific community, and our speakers<http://asca2018.org/speakers/>, and start planning your schedule. It's peak season in December so we recommend you book your accommodation<http://asca2018.org/accommodation/> early. Likewise, if you haven't submitted your abstract yet, we kindly request your support by submitting contributions to the AsCA 2018/CRYSTAL 32 conference at your earliest convenience before the deadlines (1 September 2018 for Oral, 1 November 2018 for Poster). The online abstract submission link is http://asca2018.org/call-for-abstracts/. The conference will run from 2-5 December 2018. We look forward to seeing you there. In the meantime, if you have any questions please visit the conference website<http://asca2018.org/> or contact us via email<mailto:[email protected]?subject=AsCA%20inquiry>. Kind regards, Dr. Christopher Squire (University of Auckland), Professor Ted Baker (University of Auckland), Professor Kurt Krause (University of Otago) and the AsCA 2018/CRYSTAL 32 Committee. [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] ________________________________ ?

1 0

Workshop on nMX at ECM31, the programme now online
by John R Helliwell 02 Aug '18

02 Aug '18

Dear Colleagues, The Workshop on nMX at ECM31, the programme is now online at:- https://ecm31.ecanews.org/en/neutron-macromolecular-crystallography.php There is still time to register. Best wishes, John Emeritus Professor John R Helliwell DSc

1 0

Error building Amber interface to phenix
by Roger Shek 30 Jul '18

30 Jul '18

I am trying to build the amber interface to phenix, but encounter an error. Running OpenSUSE15. Anyone have any ideas? phenix.build_amber_interface Phenix modules found : /opt/phenix-1.13-2998/modules/phenix $AMBERHOME set : /home/roger/bin/Amber/amber18 Linking AMBERHOME to Phenix modules Not linking $AMBERHOME into Phenix modules directory because there is already a link and it points to the same directory as $AMBERHOME. $AMBERHOME : /home/roger/bin/Amber/amber18 Phenix link: /opt/phenix-1.13-2998/modules/amber Building amber_adaptbx ~> libtbx.configure amber Python: 2.7.14 "/opt/phenix-1.13-2998/base/bin/python2.7" Compiler: default Build mode: release Warning level: 0 Precompiled Headers: False Static libraries: False Static exe: False Scan Boost headers: False Write full flex_fwd.h files: False Build Boost.Python extensions: True Define BOOST_PYTHON_NO_PY_SIGNATURES: False Define BOOST_PYTHON_BOOL_INT_STRICT: True Enable OpenMP if possible: False Boost threads enabled: False Enable CUDA: False Use opt_resources if available: False Use environment flags: False Enable C++11: False Python3 migration warning policy: None command_version_suffix: 1.13-2998 Relocatable paths anchored at: /opt/phenix-1.13-2998/build Top-down list of all modules involved: prime "/opt/phenix-1.13-2998/modules/cctbx_project/prime" iota "/opt/phenix-1.13-2998/modules/cctbx_project/iota" xia2 "/opt/phenix-1.13-2998/modules/xia2" xfel "/opt/phenix-1.13-2998/modules/cctbx_project/xfel" dials "/opt/phenix-1.13-2998/modules/dials" simtbx "/opt/phenix-1.13-2998/modules/cctbx_project/simtbx" cma_es "/opt/phenix-1.13-2998/modules/cctbx_project/cma_es" labelit "/opt/phenix-1.13-2998/modules/labelit" rstbx "/opt/phenix-1.13-2998/modules/cctbx_project/rstbx" spotfinder "/opt/phenix-1.13-2998/modules/cctbx_project/spotfinder" annlib+adaptbx "/opt/phenix-1.13-2998/modules/annlib" "/opt/phenix-1.13-2998/modules/annlib_adaptbx" phenix "/opt/phenix-1.13-2998/modules/phenix" reel "/opt/phenix-1.13-2998/modules/reel" wxtbx "/opt/phenix-1.13-2998/modules/cctbx_project/wxtbx" phaser_regression "/opt/phenix-1.13-2998/modules/phaser_regression" phaser "/opt/phenix-1.13-2998/modules/phaser" tntbx "/opt/phenix-1.13-2998/modules/tntbx" solve_resolve "/opt/phenix-1.13-2998/modules/solve_resolve" muscle "/opt/phenix-1.13-2998/modules/muscle" ksdssp "/opt/phenix-1.13-2998/modules/ksdssp" pulchra "/opt/phenix-1.13-2998/modules/pulchra" phenix_html "/opt/phenix-1.13-2998/modules/phenix_html" phenix_regression "/opt/phenix-1.13-2998/modules/phenix_regression" elbow "/opt/phenix-1.13-2998/modules/elbow" Plex "/opt/phenix-1.13-2998/modules/Plex" PyQuante "/opt/phenix-1.13-2998/modules/PyQuante" crys3d "/opt/phenix-1.13-2998/modules/cctbx_project/crys3d" gltbx "/opt/phenix-1.13-2998/modules/cctbx_project/gltbx" amber+adaptbx "/opt/phenix-1.13-2998/modules/amber" "/opt/phenix-1.13-2998/modules/amber_adaptbx" mmtbx "/opt/phenix-1.13-2998/modules/cctbx_project/mmtbx" suitename "/opt/phenix-1.13-2998/modules/suitename" king "/opt/phenix-1.13-2998/modules/king" probe "/opt/phenix-1.13-2998/modules/probe" reduce "/opt/phenix-1.13-2998/modules/reduce" iotbx "/opt/phenix-1.13-2998/modules/cctbx_project/iotbx" ccp4io+adaptbx "/opt/phenix-1.13-2998/modules/ccp4io" "/opt/phenix-1.13-2998/modules/ccp4io_adaptbx" dxtbx "/opt/phenix-1.13-2998/modules/cctbx_project/dxtbx" cbflib+adaptbx "/opt/phenix-1.13-2998/modules/cbflib" "/opt/phenix-1.13-2998/modules/cctbx_project/cbflib_adaptbx" smtbx "/opt/phenix-1.13-2998/modules/cctbx_project/smtbx" ucif "/opt/phenix-1.13-2998/modules/cctbx_project/ucif" cctbx "/opt/phenix-1.13-2998/modules/cctbx_project/cctbx" scitbx "/opt/phenix-1.13-2998/modules/cctbx_project/scitbx" fable "/opt/phenix-1.13-2998/modules/cctbx_project/fable" omptbx "/opt/phenix-1.13-2998/modules/cctbx_project/omptbx" boost+adaptbx "/opt/phenix-1.13-2998/modules/boost" "/opt/phenix-1.13-2998/modules/cctbx_project/boost_adaptbx" tbxx "/opt/phenix-1.13-2998/modules/cctbx_project/tbxx" chiltbx "/opt/phenix-1.13-2998/modules/cctbx_project/chiltbx" libtbx "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx" Processing: "/opt/phenix-1.13-2998/build/dispatcher_include_amber.sh" Processing: "/opt/phenix-1.13-2998/build/dispatcher_include_phenix.sh" Creating files in build directory: "/opt/phenix-1.13-2998/build" dispatcher_include_template.sh dispatcher_head.sh Traceback (most recent call last): File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 2462, in <module> warm_start(sys.argv) File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 2456, in warm_start env.refresh() File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 1615, in refresh self.write_lib_dispatcher_head() File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 1248, in write_lib_disp atcher_head target_file=self.under_build(target_file, return_relocatable_path=True)) File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 1146, in write_bin_sh_d ispatcher target_file.chmod(0755) File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/path.py", line 279, in chmod return os.chmod(abs(self), *args, **kwds) OSError: [Errno 1] Operation not permitted: '/opt/phenix-1.13-2998/build/dispatcher_head.sh' -- Roger Shek Stony Brook University Graduate Student in Biochemistry and Structural Biology (PhD) Stony Brook Integrative Structural Biology Organization <http://sbinststrbio.com/> Cell: (808) 386-3879 Website: https://www.rogershek.com

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Ligand occupancy and conformational change
by Xavier Brazzolotto 24 Jul '18

24 Jul '18

I am struggling with a ligand bound structure. The ligand seems to induce a small conformational change of one loop. However, despite my efforts I did not get any data with a full occupancy for this ligand yet. As a result, I have to deal with a loop in apo state (where ligand occupancy = 0) and a loop with a bound ligand (where ligand occupancy <1) and where the ligand is clashing with the modelled loop in the apo state. Hope I did myself clear. How to deal with this situation ? I am sure that phenix.refine can do it but how ? What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X Maybe something specific in a parameter file ? Thank you for your help Xavier

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How to use phaser gyre and gimble in phenix
by Meinke, Gretchen 19 Jul '18

19 Jul '18

Hello again-- I have partially solved my silly problem: This is how to use it. phenix.gyre_and_gimble I may write back for more specifics, if my MR remains unsolved. Thanks! Gretchen

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How to use phaser gyre and gimble in phenix
by Meinke, Gretchen 18 Jul '18

18 Jul '18

Hi! I have a challenging MR problem and maybe phenix.phaser gyre and gimble will help. My molecule is flexible horsehoe shaped slinky, there are multiples in the unit cell (maybe 8-12??). My data is medium resolution 3.5 maybe. There are good homology models (also flexible!) It seems to have 1-2 hinge points (or 2-3 domains). I saw your publication "Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement" Acta Cryst. (2018). D74, 279–289 and that describes exactly what I would like to do. One problem, I cannot at all figure out how to use gyre in gimble in phenix. I cannot find it in the GUI, and am unclear how to run it as a script. It looks super useful and would love to use it. Any help, a script, etc would be most appreciated! Thanks! Gretchen

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