- phenixbb - phenix-online.org

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

2 1

Recruiting fragment/XChem crystallographers
by Frank von Delft 22 Sep '18

22 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)

1 0

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.)

1 0

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

3 2

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.

2 1

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.

2 1

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.

3 3

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…]

1 0

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)

4 3

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

1 0