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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.*

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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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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 > >

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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.

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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…] ________________________________ ?

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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

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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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