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single atom mmcif bug
by Edwin Pozharski 06 Sep '18

06 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 05 Sep '18

05 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 25 Aug '18

25 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 23 Aug '18

23 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 23 Aug '18

23 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 22 Aug '18

22 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 21 Aug '18

21 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.*

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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

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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 > > > > > > > > >

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