- phenixbb - phenix-online.org

Call for not-yet-released structures as candidates for protein structure predictors
by Susan Tsutakawa 17 Apr '18

17 Apr '18

Critical Assessment of Techniques for Protein Structure Prediction (CASP) community experiments aim to advance the state of the art in protein structure modeling. Every other year since 1994, CASP collects information on soon-to-be released experimental structures, passes on sequence data to the structure modeling community, and collects blind predictions of structure for assessment. About 100 modeling groups from around the world participate. Results of CASP experiments are published in special issues of the journal PROTEINS (e.g., CASP12: Proteins Vol 86, Issue S1, March 2018). The thirteenth CASP round is scheduled to start on May 1, 2018. The organizing committee is particularly keen to include many cryo-EM-derived structure targets in this round. The success of CASP depends on the generosity of the structure determination community. Modeling targets are needed over a wide range of difficulty, for modeling both with and without the aid of templates. Targets that can be modeled based on structural templates should ideally have 50% or less sequence identity to the templates. Access to the structure in advance of its release by the PDB or its publication is not needed. With sufficient notification to CASP (a minimum of three weeks before release, more is better) there is no need to delay structure release. If you have recently determined a novel protein structure and will be depositing it to PDB, please suggest it as a target for CASP by visiting www.predictioncenter.org/casp13/targets_submission.cgi. If you have any questions please contact [log in to unmask] CASP target providers are regularly invited to contribute to special issue papers, for example: 2018: Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. (2018). Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 86 (S1), 27-50. doi: 10.1002/prot.25392. PMID: 2896053 2016: Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. (2016). Some of the most interesting CASP11 targets through the eyes of their authors. Proteins 84 (S1), 34-50. doi: 10.1002/prot.24942. PMID: 26473983 2014: Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. (2014). Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th critical assessment of techniques for protein structure prediction experiment CASP10. Proteins 82 (S2), 26-42. doi: 10.1002/prot.24489. PMID: 2431898 2011: Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. (2011). Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins 79 (S10), 6-20. doi: 10.1002/prot.23196. PMID: 2202078 Posted on behalf of the CASP organizing committee: John Moult, University of Maryland, USA Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis USA Torsten Schwede, University of Basel, Switzerland

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R-factor expectations when translational pseudo symmetry is present
by Tanner, John J. 17 Apr '18

17 Apr '18

Dear PhenixBB, We have a crystal form that xtriage flags as having strong translational pseudo symmetry (Patterson peak 57% the height of the origin peak, p-value = 3E-5). The space group is P21212. We can solve the structure with MR and refine to R=0.233 and R-free =0.276 at 2.25 Angstrom resolution. The maps look very good, but do not suggest major additional modeling that could be done to improve the structure and lower the R-factors. I know that one expects the R-factors from refinement to be higher when TPS is present, but my question is how high is too high? Has anyone done a study that shows the expectations for R-factors when TPS is present? Thanks, Jack John J. Tanner Interim Chair, Department of Biochemistry Professor of Biochemistry and Chemistry Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-5635 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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Trouble running getting ERRASER to run
by Shintaro Aibara 17 Apr '18

17 Apr '18

*Dear PhenixBB,* *I am trying to get ERRASER to run and am struggling a bit. I was wondering if somebody could point me in the right way. Apologies if this has been asked before - my Google-Fu is inadequate.* *Phenix Version: dev-3092* *Rosetta Version: 2018.09.60072* *I built rosetta using scons as per the instructions online and fired rosetta.build_phenix_interface with no errors. I've identified that the erraser directory lives in main/source/src/apps/public/ERRASER and accordingly set my environmental variables.* *Being fairly clunky around the linux environment, I am probably doing something very silly. Any help would be much appreciated.* *Best wishes,* *Shintaro* *When I try to run erraser from the phenix GUI I am greeted by this error message:* TypeError : __init__() takes at least 3 arguments (1 given) Traceback (most recent call last): File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/App.py", line 784, in OnTimer self.run_manager.update(update_backgrounded=False) File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/ProcessControl.py", line 213, in update process.update() File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/wxGUI2/ProcessControl.py", line 136, in update self._process.update() File "/home/saibara/software/phenix/phenix-dev-3092/modules/cctbx_project/libtbx/runtime_utils.py", line 306, in update (error, traceback_info) = easy_pickle.load(self.error_file) File "/home/saibara/software/phenix/phenix-dev-3092/modules/cctbx_project/libtbx/easy_pickle.py", line 80, in load return cPickle.loads(_open(file_name, "rb").read()) TypeError: __init__() takes at least 3 arguments (1 given) *Alternatively if I try to fire phenix.erraser through the command line, I get something like this:* Running ERRASER Rosetta app... ################################### Path to ERRASER: /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER ERROR: Assertion `scorefxn_->get_weight( cart_bonded ) > 0` failed. ERROR:: Exit from: src/protocols/rna/movers/ErraserMinimizerMover.cc line: 238 BACKTRACE: /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2ea) [0x7f3e2b7798fa] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move(core::chemical::ResidueType const&, unsigned long const&)+0x92) [0x7f3e34c17062] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry(core::kinematics::MoveMap&, core::pose::Pose&, ObjexxFCL::FArray1D<bool>&, std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > const&)+0x20a) [0x7f3e34c1771a] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols_d.6.so(protocols::rna::movers::ErraserMinimizerMover::apply(core::pose::Pose&)+0x2020) [0x7f3e34c20f70] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xbed) [0x7f3e344cc9bd] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x166) [0x7f3e344cedc6] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/default/ libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x57) [0x7f3e344b4d67] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x40480e] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4037b1] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f3e32bdc830] /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease() [0x4045b9] Traceback (most recent call last): File "/home/saibara/software/phenix/phenix-dev-3092/build/../modules/phenix/phenix/command_line/erraser.py", line 14, in <module> erraser_run=phenix.erraser.erraser.erraser(args=sys.argv[1:]) File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/phenix/erraser/erraser.py", line 349, in __init__ self.run(params,out=out) File "/home/saibara/software/phenix/phenix-dev-3092/modules/phenix/phenix/erraser/erraser.py", line 459, in run erraser(option) File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 99, in erraser erraser_minimize( minimize_option ) #full_struct_slice_and_minimize( minimize_option ) File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_wrapper.py", line 478, in erraser_minimize subprocess_call(command, sys.stdout, sys.stderr) File "/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/src/apps/public/ERRASER/erraser_util.py", line 107, in subprocess_call subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel) File "/home/saibara/software/phenix/phenix-dev-3092/base/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/source/bin/erraser_minimizer.linuxgccrelease -database /home/saibara/software/rosetta/rosetta_bin_linux_2018.09.60072_bundle/main/database/ -s /home/saibara/Phenix/hsmitoribo_drug/rnaonly_erraser_temp/minimize_0.pdb -score:weights stepwise/rna/rna_hires_elec_dens_FCC2012 -score:rna_torsion_potential FCC2012_RNA11_based_new -rna::corrected_geo true -rna::erraser::rna_prot_erraser false -rna::vary_geometry true -constrain_P true -attempt_pyrimidine_flip false -rna::erraser::skip_minimize false -chemical:enlarge_H_lj false -in:guarantee_no_DNA false -out:file:write_pdb_link_records true -scale_d 100 -scale_theta 10 -stepwise:rna:o2prime_legacy_mode true -use_2prime_OH_potential false -edensity:mapfile /home/saibara/Phenix/hsmitoribo_drug/cheatmap.ccp4 -edensity:mapreso 3.0 -edensity:realign no -graphics false -skip_connect_info true ' returned non-zero exit status 255

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Final reminder: 11th CCP4/APS Crystallographic School in the US June 18 through 25, 2018
by Qingping Xu 16 Apr '18

16 Apr '18

Dear Colleagues, This is a reminder for the upcoming CCP4/APS school. The deadline for registering is coming up soon, please register if you plan to attend. Thanks. Charles, Garib and Qingping ====original announcement ==== Dear Colleagues, We are pleased to announce the *11th annual CCP4 crystallographic school *“From data collection to structure refinement and beyond” will be held on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php. *Dates*: June 18 through 25, 2018 *Location*: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: *data collection workshop* and *crystallographic computing workshop*. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is *Wednesday May 2nd, 2018*. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php *Registration fees*: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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Running on Windows 10
by Plínio Salmazo Vieira 15 Apr '18

15 Apr '18

Dear all I'm having issues on running Phenix. It installs smoothly (I downloaded the point-and-click 64-bit version), but when I try to open, the prompt writes very fast and closes by itself. I tried installing and running on administrator mode and on compatibility mode for Windows 7, but still no good. Below are my laptop configuration: Processor: Intel Core it-7500U CPU @ 2.70 GHz 2.90 GHz RAM: 8 GB System: Operational based on 64 bits, processor x64 Please, could anyone help me? Any guesses? If you need any more information, let me know. Best Regards, Plínio. -- Dr. Plínio Salmazo Vieira Laboratório Nacional de Ciência e Tecnologia do Bioetanol Centro Nacional de Pesquisa em Energia e Materiais Campinas - São Paulo

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Polder comment
by Patrick Loll 14 Apr '18

14 Apr '18

What does it mean when a Polder map calculation finishes with the comment "The polder map is more likely to show bulk-solvent or noise instead of the ligand” ? Thx, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjloll(a)gmail.com pjl28(a)drexel.edu

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Unflagging accidental "Mark as Failed" in GUI
by Shane Caldwell 13 Apr '18

13 Apr '18

Hi phenixbb, I have a mostly inconsequential and hopefully simple problem to solve, but I can't find info about it online. I accidentally flagged a good run as "failed" in the Phenix GUI, and I can't figure out how to remove that tag. It's possible I'm overlooking something extremely obvious and if so apologies for the spam. How can I reset this marker? Shane Shane Caldwell shane.caldwell17(a)gmail.com

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AsCA 2018/CRYSTAL 32: Registration Open!
by Christopher Squire 11 Apr '18

11 Apr '18

? [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] Dear Colleagues, Registration for the AsCA 2018/CRYSTAL 32 Conference (2 - 5 December 2018 at the University of Auckland, New Zealand) is now open! Please follow this link to register http://asca2018.org/registration/ Workshop registration is not yet open, however please use the voting function here<http://asca2018.org/workshops/> to advise which of the four potential workshops would be of most interest to you. Finally, a reminder that submissions are now open. Please visit the Call for Abstracts<http://asca2018.org/call-for-abstracts/> page for more information and to submit an abstract. Should you have any queries regarding the AsCA 2018/CRYSTAL 32 Conference, please do not hesitate to contact us using the email address listed below. Kind regards, Event Services University of Auckland Email: asca2018(a)auckland.ac.nz<mailto:[email protected]> [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…]

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Phenix video tutorials
by Dorothee Liebschner 10 Apr '18

10 Apr '18

Dear Phenix users, This is an update for the Phenix video tutorials. There are now 25 videos, explaining Phenix tools for X-ray crystallography and cryo-EM. New videos include topics such as model and data validation (Xtriage, Molprobity), phasing (Phaser, AutoSol) and tools for cryo-EM. A categorized overview is on the phenix homepage: https://www.phenix-online.org/documentation/reference/tutorial_channel.html You can also browse the videos directly 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.) Feedback about the videos is very welcome. Write an email to tutorials(a)phenix-online.org or use the comment section on YouTube. If you want to see a tutorial about a certain (Phenix-related) topic, don't hesitate to tell us. Best wishes, The Phenix team

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9th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 09 Apr '18

09 Apr '18

Second announcement 9th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 11 - June 15, 2018 Travel and accommodation expenses are supported for selected participants. No registration fee. Detailed information can be found on the workshop web page: https://conference.sns.gov/biologyneutrons18/ Application deadline: April 30, 2018 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Flora Meilleur, Ph. D Neutron Scattering Scientist, Neutron Sciences Directorate Oak Ridge National Laboratory Associate Professor, Molecular and Structural Biochemistry North Carolina State University

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FW: Announcement of European Crystallographic Computing Forum 2018 in Mieres, Spain
by Tom Terwilliger 09 Apr '18

09 Apr '18

Registration for the European Crystallographic Computing Forum is open: https://www.mrc-lmb.cam.ac.uk/harry/ecacomsig/mieres.html A poster for print can be downloaded here: https://we.tl/CyPFzYvorG Spread the word! The Forum will be held in Mieres, Spain, 18th - 22nd August 2018 (preceding the ECM). We invite both beginners (from graduate level) and experienced software developers from all crystallographic disciplines. Participants can bring their own software development project to work on it in teams, interspersed with tutorials and lectures. There will be opportunity to exchange and connect with other crystallographic software developers. The registration fee (360 €) includes: accommodation (4 nights), full board and refreshments and transfer to the ECM. We offer childcare and family rooms. Bursaries are available. We hope to see you there! The Organisers Andrea Thorn, Harry Powell, Laura Roces Fernandez We would like to thank our kind sponsors! - CCP4 - Dectris - Rigaku - Bruker -

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TaBr SAD Autosol and Phaser
by Ian S 09 Apr '18

09 Apr '18

Hi Phenixbb, I trying to phase a structure soaked in TaBr and am running into some technical problems. My anomalous signal goes out to about 4.5 and I have a 1.9A native data set. SIR hasn't worked so far. Autosol SAD has given me several convincing solutions when searching for Tantalum (not TX), finding 11 sites (not clustered) at 6 angstroms: FOM =0.478, map=0.1.3, and corr of 0.82 and a final score of 37+-15.71. By only playing around with the sites I can get an overall score of 73 +- 4.58, map skew to 0.5, and a RMS density to 0.79, thought the R-factor increases to .43 and the FOM . Perhaps not suprisingly at this resolution, the map is uninterpretable (maybe some helices) so I'm trying to improve the phases by model building and by using Phaser and giving it TX sites. If I put the Ta sites in Phaser with the same dataset as Autosol, I get a FOM of .342. If I use the TX label it drops to 0.143. What is happening here? I know that typically TaBr has one or two major sites (my protein isnt massive, only about 1200 aa predicted in the ASU) , so I use only the top two major sites and have the same problem. Does this indicate that the Ta sites Autosol found are not in fact the sites I'm looking for? Or maybe that there really are 10 TaBr sites all with low occupancy? Any suggestions would be appreciated. Thank you. Best, Ian

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linking only one conformer to a thiol
by Krzysztof Bzymek 06 Apr '18

06 Apr '18

Hi, I'm trying to refine a structure with a disulfide bond between a cysteine and a thiol-containing peptide. There are two conformations for the thiopeptide, in one of them the thiol is facing away from SG of the cysteine (~7 A away). I defined the link as: refinement.pdb_interpretation { apply_cif_link { data_link = DRG-CYS residue_selection_1 = chain A and resname DRG and resid 10 residue_selection_2 = chain B and resname CYS and resid 20 } } I also tried: refinement.pdb_interpretation { apply_cif_link { data_link = DRG-CYS residue_selection_1 = chain A and resname DRG and resid 10 and altloc A residue_selection_2 = chain B and resname CYS and resid 20 } } After refinement (with a corresponding data_link.eff file defining the bonds and angles), the thiol of the other conformer that was facing away from the cysteine moves out of the electron density and now faces the cysteine (still about ~5.7 A away). Is there a way to define a link between only one conformer and have the other refine independently? I did try refinement without the above link definition (relying on the proximity of the two cysteines and automatic linking in phenix) but some of the bond and dihedral angles showed higher deviation from ideal values expected for disulfide bonds. Thanks, Chris

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23rd Annual SCSB Symposium, April 28th, Galveston Texas
by Mark A. White 04 Apr '18

04 Apr '18

You and your colleagues are cordially invited to join us for the 23rd Annual Structural Biology Symposium to be held at Levin Hall on the University of Texas Medical Branch Campus on beautiful Galveston Island on Saturday, April 28, 2018. The meeting is organized by the Sealy Center for Structural Biology & Molecular Biophysics and co-sponsored by the Keck Center for Computational & Structural Biology. This year’s speakers include: Grant Jensen, Ph.D., California Institute of Technology “Progress and Challenges in Electron Cryotomography” Ayyalusamy Ramamoorthy, Ph.D., University of Michigan “Membrane-Assisted Dynamic Protein-Protein Interactions by NMR" Andrew Routh, Ph.D., University of Texas Medical Branch “Parallel ClickSeq and Nanopore Deep-Sequencing Characterizes the Emergence and Evolution of Defective Viral Genomes” Joan-Emma Shea, Ph.D., University of California Santa Barbara “Binding and Assembly of Intrinsically Disordered Peptide” Yizhi Tao, Ph.D., Rice University “The Tail of a Nematode Virus” Adam Zlotnick, Ph.D., Indiana University “Multiple Mechanisms for Assembly-Directed HBV Antivirals” To register or for more information, visit http://scsb.utmb.edu/symposium -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.658A University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 mailto://[email protected] http://xray.utmb.edu QQ: "For a man to conquer himself is the first and noblest of all victories." - Plato

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Rfree and a low resolution data set
by Toon Van Thillo 04 Apr '18

04 Apr '18

Hi all, Currently I am refining a data set which showed anisotropic diffraction. Aimless suggested cutoffs at 2.3, 2.6 and 3.6 angstrom for the h,k and l axis. I chose a general 3.6 cutoff to obtain satisfactory statistics for Rmeas, I/sd(I) and CC1/2. At this resolution the data set consists of approximately 2800 reflections. Generally 5% of the set is set aside as the Rfree test set and I found that a minimum of 500 reflections in total is used to produce a reliable Rfree. However, 5% only amounts to 140 reflections in this case. I am hesitant to include more reflections as I would have to go up to 20% of the reflections to obtain more than 500 reflections for the test set. In a discussion on the CCP4 message boards some time ago it was suggested to do multiple refinements with different test sets: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1411&L=ccp4bb&F=&S=&P=125… In the thread it was also discussed that a least squares approach is prefered when using a small test set. However, when using a LS target, the resulting Rfree is very high (10% higher than when using the automatic option) and phenix.refine? produces awful geometry (24% ramachandran outliers, 105 clashcore...). It seems that the refinement is performed without restraints? Optimize X-ray/stereochemistry weight does not result in improved stereochemistry. My question is if the LS approach is still relevant and if so, is there an explanation (and solution) for the bad statistics? Kind regards, Toon Van Thillo

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A new capability on the STARANISO server: "PDBpeep"
by Gerard Bricogne 29 Mar '18

29 Mar '18

Dear all, Ever since the WebGL viewer became available on the STARANISO server, we have found ourselves using it with increasing frequency to take a quick look (a "peep") at the diffraction data deposited with various PDB entries - for example, to try and identify a root cause for some sub-optimal refinement results, or, quite often, just out of sheer curiosity! This involved a totally straightforward procedure whereby the diffraction data file associated with a given PDB entry was downloaded from the PDB and subsequently uploaded to the STARANISO server. Gradually, however, this operation became so popular among some of us that we thought it would be useful to implement this simple procedure as an autonomous capability - and thus was born "PDBpeep" ! You can access this new feature by connecting to http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi and enter a PDB code into the box. As indicated on that page, this provides only a cursory look at the overall quality of each dataset, and any further analysis or output can only be obtained by submitting the datafile to the STARANISO server. Better results would clearly be obtainable if the raw images for these datasets had been deposited and could be reprocessed, with the untruncated output of that processing then being submitted to the STARANISO server (reprocessing the images with autoPROC would combine those two steps into a single one). Most of the deposited datasets have been isotropically truncated, and their 3D view in WebGL often suggests that this truncation was too drastic. A number of entries will show infelicities - such as cusps and/or missing angular ranges, or even stripes caused by gaps between the modules of pixel detectors if the beam centre is at a position symmetric relative to those gaps - all marked up in blue. Our purpose in sharing this capability with the community is to bring a further contribution to the process of making everyone more "data quality aware" and keen to scrutinise more closely the protocols by which they collect diffraction data, or have such data collected on their behalf. We will be grateful to receive feedback about PDBpeep, just as we have been about the STARANISO server itself. With best wishes, The STARANISO developers.

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MR Rosetta fails
by Aaron Oakley 29 Mar '18

29 Mar '18

Salvete! I am trying (unsuccessfully) to run MR Rosetta. Im using a MacBookPro running OS X 10.13.3. The job terminates with Sorry: mr_rosetta failed... Sorry routine failed Please see log file for full error message The relevant log file rebuild.log terminates with protocols.jd2.JobDistributor: [ WARNING ] The following options have been set, but have not yet been used: -in:file:extended_pose 1 I get the same error with phenix-1.13-2998 and phenix-dev-3092. I'm using rosetta_bin_mac_2018.09.60072_bundle. Advice accepted with thanks. a++ Aaron Oakley Associate Professor School of Chemistry | Science, Medicine and Health University of Wollongong NSW 2522 Australia T +61 2 4221 4347 | F +61 2 4221 4287

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non-consecutive residue selection in phenix.polder
by Schulz, Eike-Christian 28 Mar '18

28 Mar '18

Dear all, To generate unambiguous ligand density in a number of structures we would like to omit the surrounding active site residues in the polder-map calculation. However, so far we were unable to figure out how non-consecutive residues can be selected for phenix.polder. https://www.phenix-online.org/documentation/reference/atom_selections.html The documentation only explains how to select ranges of residues but not how to select say 5 individual residues. Is there a syntax to achieve this ? Thanks for your advice, Eike

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iNEXT EM and X-ray bundles!
by a.perrakis＠nki.nl 26 Mar '18

26 Mar '18

Dear all, iNEXT, a European program to support access to research infrastructures for Structural Biology, is now welcoming applications for the “EM and X-ray bundles", to help people carry a project all the way from the starting sample to the initial structure determination, by EM or X-rays. To apply for either bundle you need exciting translational research projects, for which you have the macromolecule or complex you want to study in purified soluble form, and you want to engage in structural studies. In a short application form (less than one thousand words overall), you will need to describe the background of the project in your lab and current results, the general scientific background, and the value for translational research (short term but also long term value in any short of biomedical or biotechnological application). No prior experience on either method is required. For the EM bundle, projects will start with an initial characterisation for optimal stability conditions, molecular weight in solution, and negative stain EM (if you send enough sample, we can also try to crystallise it if you wish - just in case!). At this stage you will only need to send the sample to us. Projects that look most promising after that first step, will proceed to optimising the cryo-conditions in one of the iNEXT EM facilities, with your participation. Finally, projects that do best in cryo-optimisation, will proceed to collect data in one of the high-end microscopes available to iNEXT. For the X-ray bundle, projects will start with an initial characterisation for optimal stability conditions, molecular weight in solution, and crystallisation trials. Projects that either yield crystals, or promising precipitates, will proceed to extensive crystallisation trials. For all projects that will yield crystals diffraction data will be collected in one of the fully automated X-ray facilities that collaborate in iNEXT. You will only need to send the sample to us and in most cases physical presence will not be required. It should be emphasised, that no re-application will be needed at any step and iNEXT will cover all experimental expenses, and contribute to travel costs, when needed. There is a single deadline on Friday 20th April 2018. You can Submit a Proposal by clicking here<https://www.structuralbiology.eu/submit-proposal/?t=inext> or go to the iNEXT web site: http://www.inext-eu.org and follow the “Submit Proposal” link. Please note, that given the iNEXT resources availability, this is likely the only call for these “bundle” access. These will serve as pilots for likely requesting future funding from the EU, if such an opportunity becomes available. We note that researchers from all EU and associated countries can apply, but also international labs are eligible, albeit in a more limited capacity. Please forward this email beyond this bulletin list, especially to colleagues that might be less familiar with structural biology. Consider asking this colleague of yous that wanted to do a structural biology project and you never had time or the resources to try hers or his exciting idea! Preliminary results from this bundle access, or a structure, can be the basis for your next grant application! Please also keep in mind that iNEXT remains open to all kinds of Structural Audit, Enhanced Support, and High-End data collection, for projects that involve X-ray Crystallography, SAXS, solution and solid state NMR, EM single particles, EM tomography or CLEM, biophysics for looking at macromolecular interactions, advanced light imaging, and ligand and fragment screening! All these access modalities are listed on our web site! Best regards and looking forward receiving your project, The iNEXT coordination and management team and all iNEXT partners

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Phaser.find_anomalous_substructure error
by Janine Gray 24 Mar '18

24 Mar '18

Hi, I am trying to run phaser.find_anomalous_substructure to identify the anomalous peaks of some phosphorus atoms and get the following error: AttributeError: 'NoneType' object has no attribute 'as_pdb_string' Looking in the log file), it states a file opening error with my PDB file: ****************************************************************************************** *** Phaser Module: AUTOMATED EXPERIMENTAL PHASING 2.8.1 *** ****************************************************************************************** ** Steps: ** Anisotropy correction ** Experimental Phasing ** SAD Phasing CPU Time: 0 days 0 hrs 0 mins 0.02 secs ( 0.02 secs) Finished: Fri Mar 23 15:23:15 2018 ****************************************************************************************** *** Phaser Module: SINGLE-WAVELENGTH ANOMALOUS DISPERSION 2.8.1 *** ****************************************************************************************** Keyword input too long to echo to output (>10000 characters) ------------------------------------------------------------------------------------------ FILE OPENING ERROR: ATOM 1 N MET A 1 5.825 -12.222 -3.663 1.00 89.47 N Has anyone seen this before and/or knows how to fix this? Cheers, Janine

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nucleic acid secondary structure restraint sigmas
by Dyda 23 Mar '18

23 Mar '18

Hi, Does anyone one whether is it possible (and if so how) to change the target sigmas of the H-bonds restraining base pairs? It seems that base pair restraints can do several things: base_pair { enabled = True base1 = chain 'C' and resid 21 base2 = chain 'D' and resid 5 saenger_class = 19 restrain_planarity = False planarity_sigma = 0.176 restrain_hbonds = True restrain_hb_angles = True restrain_parallelity = True parallelity_target = 0 parallelity_sigma = 0.0335 What I'd like to know whether the restrain_hbonds and restrain_hb_angles sigmas can be adjusted. Or is it the case that parallelity_sigma is doing what I'm looking for? Thanks! Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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11th CCP4/APS Crystallographic School in the US
by Qingping Xu 22 Mar '18

22 Mar '18

Dear Colleagues, We are pleased to announce the *11th annual CCP4 crystallographic school *“From data collection to structure refinement and beyond” will be held on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php. *Dates*: June 18 through 25, 2018 *Location*: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: *data collection workshop* and *crystallographic computing workshop*. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is *Wednesday May 2nd, 2018*. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php *Registration fees*: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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Fwd: [ccp4bb] Xtriage anomalous signal measurement- mosflm data processing
by Pavel Afonine 22 Mar '18

22 Mar '18

---------- Forwarded message ---------- From: *Manoj Saxena* <00001d16aa30e8a1-dmarc-request(a)jiscmail.ac.uk> Date: Wednesday, March 21, 2018 Subject: [ccp4bb] Xtriage anomalous signal measurement- mosflm data processing To: CCP4BB(a)jiscmail.ac.uk Hi all, I have a dataset for which I got the .sca file from a collaborator and I am trying to look at the strength of the anomalous signal. Looking at archives in the CCP4bb I found many people suggesting using the Chi**2 values using ScaLAPACK using HKL2000. However, at the moment, I have access only to Xtriage from Phenix which gives a clear graph showing that my data has no significant difference anomalous signal. So my question is how reliable is this analysis by Xtriage and is it possible that during data processing anomalous scattering difference was lost. I would like to reprocess the data using mosflm any suggestions for data processing (to see the anomalous signal) would be appreciated. Thanks Manoj Saxena Postdoc University of Puerto Rico

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Phenix.Refine: Missing High Resolution Data
by Mark A. White 16 Mar '18

16 Mar '18

Hello, I have several data sets which seem to loose completeness in their high-resolution shells when the HKL *.sca file is converted into an MTZ. I am using the recommended Diederichs CC1/2 cut off of 0.5, which is usually an I/s <2. I also have an usually high redundancy in these data sets, not sure if that has any effect. Here is a typical comparison of the Phenix statistics and the HKL values. Note that the resolution bins do not match, and that the Phenix refinement was truncated to 3.0Å. PHENIX HKL2000/Scalepack RESOLUTION RANGE COMPL total CC1/2 CC* Redn ScP-Angstrom 50.1353 - 8.8720 97 97.8 0.989 0.997 10.9 70.00 7.87 8.8720 - 7.0483 99 - 7.0483 - 6.1591 100 99.6 0.990 0.997 12.8 7.87 6.25 6.1591 - 5.5968 100 99.7 0.991 0.998 12.9 6.25 5.46 5.5968 - 5.1961 99 - 5.1961 - 4.8900 99 99.6 0.991 0.998 13.0 5.46 4.96 4.8900 - 4.6453 99 99.5 0.986 0.996 12.9 4.96 4.60 4.6453 - 4.4432 99 99.2 0.990 0.997 13.1 4.60 4.33 4.4432 - 4.2723 99 - 4.2723 - 4.1249 99 99.8 0.988 0.997 13.3 4.33 4.11 4.1249 - 3.9960 99 99.9 0.989 0.997 13.4 4.11 3.94 3.9960 - 3.8818 99 99.9 0.987 0.997 13.5 3.94 3.78 3.8818 - 3.7796 100 - 3.7796 - 3.6875 100 99.8 0.985 0.996 13.4 3.78 3.65 3.6875 - 3.6037 100 100.0 0.975 0.994 13.5 3.65 3.54 3.6037 - 3.5270 100 - 3.5270 - 3.4565 100 100.0 0.964 0.991 13.5 3.54 3.44 3.4565 - 3.3912 100 - 3.3912 - 3.3307 97 99.9 0.966 0.991 12.1 3.44 3.35 3.3307 - 3.2742 87 100.0 0.916 0.978 10.2 3.35 3.27 3.2742 - 3.2214 68 100.0 0.857 0.961 8.5 3.27 3.19 3.2214 - 3.1719 54 - 3.1719 - 3.1252 41 100.0 0.763 0.930 7.4 3.19 3.12 3.1252 - 3.0812 33 99.9 0.616 0.873 6.4 3.12 3.06 3.0812 - 3.0396 24 - 3.0396 - 3.0001 18 98.4 0.547 0.841 5.8 3.06 3.00 95.1 0.307 0.685 5.2 3.00 2.95 89.8 0.302 0.681 4.8 2.95 2.90 98.9 0.982 0.995 10.9 All reflect. -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.658A University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 mailto://[email protected] http://xray.utmb.edu QQ: "Don’t persist in folly. Some people commit themselves to their errors. They commit one error and consider it constancy to go on that way." - Baltasar Gracian (1658)

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cis-Pro and trans-Pro refinement
by 张士军 16 Mar '18

16 Mar '18

Dear all I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro is gone when I set the "threshold degrees for cis-peptide " from default 45 to 65, but still has cis-Pro. While no significant change when I set it to 15. My question is how to set in phenix refinement in phenix GUI to clear the Pro residues in cis- or trans- conformations. Best Regards shijun

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Phenix refine ligand with alt conf and occupancy<1
by Leonhard Kick 16 Mar '18

16 Mar '18

Dear all, I'm currently working on a structure with a series of ligands which have occupancies of ~80% (according to phenix.refine). So far so good, a few of these also show alternate conformations which I'd like to let phenix refine as well, but phenix.refine adjusts the occupancy of the whole ligand (conformation A+B) automatically to 1. I see that this is useful in most cases, but not in this one. Is there a possibility to adjust the overall occupancy or another work-around that anyone can suggest? Thank you Best Leo -- ================================================== Leonhard Kick AG Schneider Technische Universität München Dept. Chemistry, Chair of Biochemistry Lichtenbergstr. 4 D-85748 Garching b. München +49 89 289 13359 leonhard.kick(a)tum.de ==================================================

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Real space refinement of complete virus structure
by #TOFAYEL AHMED# 13 Mar '18

13 Mar '18

Dear all, I am trying to refine a complete virus pdb structure (possessing icosahedral symmetry) in a cryo-EM map using phenix.real_space_refine. The run fails complaining "Multi-model PDB (with MODEL-ENDMDL) is not supported". So, I followed a previous post in phenixbb: http://www.phenix-online.org/pipermail/phenixbb/2011-May/017079.html and merged multiple models into one but faced following problems: 1. This merged file is unreadable in UCSF Chimera. 2. The secondary structure definition in the PDB file header is not recognizable anymore in Phenix. In my understanding, both the problems are arising due to PDB format's inability to handle more than 62 chains and 99999 atoms in a file. So, what will be the work-around to perform a real space refinement of the complete virus structure at once? Also, how to maintain secondary structure during such refinement? Any help is highly appreciated. Best regards, Tofayel ............................................ Tofayel Ahmed Graduate Student (PhD) | Lab-02n-01 School of Biological Sciences Nanyang Technological University 60 Nanyang Drive, Singapore 637551 +65 8650.0473 |tofayel001(a)e.ntu.edu.sg<mailto:[email protected]>

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AutoSol Br SAD/MAD
by Ian Slaymaker 12 Mar '18

12 Mar '18

Hello Phenixbb, I've been out of the crystallography game for a few years and was hoping for some suggestions. I'm trying to phase a structure (~1200aa protein:DNA complex) with native data out to 2.0A and SAD/MAD data out to 3.0-2.6. I'm trying to use Br/I soaking while I wait for Sel-Met crystals to grow. I'm collecting 1800 frames at a synchrotron and scaling together multiple MAD wavelength sets (30 degree inverse wedges) collected from the same crystal with phenix.scale_and_merge to achieve >85% anomalous data (determined by xtriage). Anomalous signal of the merged data is around 10 at the 3.5 angstrom shell. I'm keeping an eye on the merging statistics, but I'm not sure what the critical stats to monitor are. AutoSol has given me a a few possible solutions, finding between 3 and 8 sites for MAD and SAD sets(I'm letting AutoSol decide how many to find) with Resolve Rfactors around 0.34, but low map skew (<1 and sometimes negative). I've tried using the initial sites to search for additional Br sites, but with no luck, and the density isn't good enough to build anything into. I'm doing hyss searches with various resolution cutoffs and continue to get the same/similar uninterpretable density with very few heavy atom sites found. My questions: What are the critical stats to look at when merging data for anomalous signal? Are there parameters to explore in AutoSol to identify more heavy atom sites? Should I accept that I need to wait for new crystals to grow or keep charging ahead with this data, encouraged by some promising numbers by AutoSol? Thank you in advance for the suggestions. -Ian

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View Solvent Mask
by ben flath 09 Mar '18

09 Mar '18

Hi All I was watching the YouTube tutorial on Polder Maps and noticed that the bulk solvent mask was visualized in coot. How can I visualize my bulk solvent mask? Regards Ben Flath

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Re: [phenixbb] View Solvent Mask
by Flath, Ben 09 Mar '18

09 Mar '18

It seems I am looking for the the compute_box option in polder maps. Ben Sent from my Android -------- Original message -------- From: "Flath, Ben" <bef206(a)mail.usask.ca> Date: 2018-03-09 11:15 AM (GMT-06:00) To: Pavel Afonine <pafonine(a)lbl.gov>, "Flath, Ben" <bef206(a)mail.usask.ca>, phenixbb(a)phenix-online.org Subject: Re: [phenixbb] View Solvent Mask Now the important question How can I modify the mask so it doesn't enter pockets within my model? Add HOH with occupancy set to zero and ignore_zero_occupancy_atoms=False? Or is running polder maps more effective? Thanks again Ben Sent from my Android -------- Original message -------- From: Pavel Afonine <pafonine(a)lbl.gov> Date: 2018-03-09 10:50 AM (GMT-06:00) To: "Flath, Ben" <bef206(a)mail.usask.ca>, phenixbb(a)phenix-online.org Subject: Re: [phenixbb] View Solvent Mask Hi Ben, I was watching the YouTube tutorial on Polder Maps and noticed that the bulk solvent mask was visualized in coot. How can I visualize my bulk solvent mask? phenix.mask model.pdb will calculate the mask. Pavel

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Questions about the Autosol water placing option
by Kaibo Zhang 07 Mar '18

07 Mar '18

Helllo, I was using AutoSol GUI for MR-SAD of my data and trying to turn off "place waters in refinement". However, the output pdb files still got waters in them. I did check the run log file and confirmed both the "place_waters" and the "flood_with_waters" flags were set to false. But in the later session, it still recorded "adding waters in refinement". Is there any parameters I should adjust to avoid adding waters during the Autosol run. Or is it just turned on in the end in order to calculate R_work/free, and doesn't affect your phasing solution? Look forward to your responses. Thank you in advance! Regards Kaibo *Kaibo* PULSe, Purdue University Hockmeyer Hall, Room 321 240 S. Martin Jischke Drive, West Lafayette, IN 47907 Telephone: 765-337-1955 E-mail: zhang644(a)purdue.edu

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Re: [phenixbb] Overlapping ligand-protein side chain density
by van den Bedem, Henry 02 Mar '18

02 Mar '18

If the phe is a gatekeeper, shouldn’t the ligand be refined at partial occupancy; i.e. occupancies not necessarily have to ‘add up’ as you suggest? Maybe this link is helpful too: www.biorxiv.org/content/early/2018/01/24/253419 H From: <phenixbb-bounces(a)phenix-online.org> on behalf of "Phan, Jason" <jason.phan(a)vanderbilt.edu> Date: Wednesday, February 28, 2018 at 1:30 PM To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] Overlapping ligand-protein side chain density All, A piece of a ligand and the side chain of a “gate-keeper” Phe occupy the same space with well-defined features observed for both (resolution is 1.7 A). It looks about 50:50. How do you refine both ligand and protein side chain in this case? A couple of phenixbb suggestions for dealing with ligand-ligand overlapping density have been considered. With the first suggestion, the two entities still clashed and moved apart off of their respective densities. The second suggestion is not applicable in this case since the other molecule is not a ligand but part of the protein but it was tested anyway. Although there was no bumping, the occupancies don’t add up, resulting in a big blob of negative density around the ligand piece. ------------------------------ Only two comments: 1. At that resolution, constrained group occupancy refinement should work reasonably well (provided you can model the 2 entities). Then you also do not have clashes between the molecules, because Occ(A)+Occ(B)=1, meaning when one (A) is there, the other one (B) is not. This works with refmac (external keyword file); if you need more sophisticated occupancy re/constraints SHELXL may offer more opportunities. 2. There is no necessity for the two NCS copies of the binding site to look exactly the same (non-equivalent). Maybe there is a good reason/story (accessibility, contacts etc) for one site to be occupied differently than the other one. Best, BR —————————————— Modeling two molecules that occupy overlapping binding sites in a structure simply involves designating them as alternate conformers, with the same chain and residue number, and an occupancy that sums to 1.0. For example, if you have an AMP and an ADP that occupy the same binding site, you would define them as AAMP B 501 BADP B 501 and initially set the occupancies for the atoms in each conformer to the ratio (50:50, 30:70, etc.) that you observe in the density. Refinement in this manner is straightforward in PHENIX. Diana ----------------------------

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Overlapping ligand-protein side chain density
by Phan, Jason 28 Feb '18

28 Feb '18

All, A piece of a ligand and the side chain of a “gate-keeper” Phe occupy the same space with well-defined features observed for both (resolution is 1.7 A). It looks about 50:50. How do you refine both ligand and protein side chain in this case? A couple of phenixbb suggestions for dealing with ligand-ligand overlapping density have been considered. With the first suggestion, the two entities still clashed and moved apart off of their respective densities. The second suggestion is not applicable in this case since the other molecule is not a ligand but part of the protein but it was tested anyway. Although there was no bumping, the occupancies don’t add up, resulting in a big blob of negative density around the ligand piece. ------------------------------ Only two comments: 1. At that resolution, constrained group occupancy refinement should work reasonably well (provided you can model the 2 entities). Then you also do not have clashes between the molecules, because Occ(A)+Occ(B)=1, meaning when one (A) is there, the other one (B) is not. This works with refmac (external keyword file); if you need more sophisticated occupancy re/constraints SHELXL may offer more opportunities. 2. There is no necessity for the two NCS copies of the binding site to look exactly the same (non-equivalent). Maybe there is a good reason/story (accessibility, contacts etc) for one site to be occupied differently than the other one. Best, BR —————————————— Modeling two molecules that occupy overlapping binding sites in a structure simply involves designating them as alternate conformers, with the same chain and residue number, and an occupancy that sums to 1.0. For example, if you have an AMP and an ADP that occupy the same binding site, you would define them as AAMP B 501 BADP B 501 and initially set the occupancies for the atoms in each conformer to the ratio (50:50, 30:70, etc.) that you observe in the density. Refinement in this manner is straightforward in PHENIX. Diana ----------------------------

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Plots of local real-space CC
by Murpholino Peligro 27 Feb '18

27 Feb '18

Dear all I want to get the values for the blue line (i.e. local real-space CC) in the Molprobity multicriterion plot. How can I do that? I want to plot those values with gnuplot. I do not want the whole graph (red and green lines). Thanks Murphy

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hi please unsubscribe me
by Zhenwei Su 27 Feb '18

27 Feb '18

-- Zhenwei Su 4417 Spruce Street, APT 3A Philadelphia, PA 19104 email: zwsuustc(a)gmail.com cell phone: (608) 698-4156

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hi please unsubscribe me
by Zhenwei Su 27 Feb '18

27 Feb '18

-- Zhenwei Su 4417 Spruce Street, APT 3A Philadelphia, PA 19104 email: zwsuustc(a)gmail.com cell phone: (608) 698-4156

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Issues with refinement of cadmium
by Mohammad Khan 27 Feb '18

27 Feb '18

Dear all, I am trying to fit Cd ion in a protein structure using Phenix. However, the refinement transposes CD to DC and returns me a result with DC ( 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE) in the validation report and gives me the missing atoms accordingly. When I open the same structure in Coot, it shows me the ion Cd. Also, the .pdb file contains Cd. Cd is present in my crystallization condition and fits well into the density. Other metal atoms such as Zn and Cl have refined well. HETATM 5535 CD CD F 1 156.533 -64.594 138.360 1.00 76.11 CD HETATM 5536 CD CD F 2 119.954-111.545 105.562 1.00 35.85 CD HETATM 5537 CD CD F 3 152.936 -93.077 102.747 1.00 28.68 CD HETATM 5538 CD CD F 4 121.467 -96.375 128.574 1.00 72.24 CD Can someone suggest what may be wrong? Thanks in advance!

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[Feature request] Exclude atoms outside user provided mask from refinement (in phenix.real_space_refine)
by Oliver Clarke 26 Feb '18

26 Feb '18

Hi, Often I would like to refine part of a model against a EM map generated by masked refinement. Such a map is typically better than the globally refined map in the region within the mask, and worse outside it. It would be useful to have the capacity to refine the same model first against the globally refined map, and then against the maps generated by masked refinement, but restricting refinement in the latter case to atoms/residues within the bounds of the mask. Is this something that could be maybe added in a future version of phenix.real_space_refine? This would mean allowing the user to provide a mask file, and setting an option to exclude all atoms/residues outside the mask boundaries from refinement. Cheers Oli

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refining a covalent-bound ligand
by Sebastiano Pasqualato 26 Feb '18

26 Feb '18

Hi there, I have a pretty basic question. I am refining a structure in which a drug has been covalently linked to a Cys of the protein. I have generated the .cif fie for the ligand, but I don’t know how to tell the program that carbon C04 has to be covalently linked to the SG of the Cys. Is that sufficient to insert a LINK record in the pdb file? What is the correct syntax for that? Thanks a lot for the feedback and sorry for the naive question, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEOXtalUnit

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Information regarding Anisotropic atoms
by pooja kesari 22 Feb '18

22 Feb '18

I observed that phenix.refine tool is adding anisotropic atoms to the pdb file by default even at resolution more than 2A. Can anyone please suggest why is it doing so?

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lattice symmetry and free-set selection?
by Edward A. Berry 22 Feb '18

22 Feb '18

Where can I find description of the free-r selection parameters: refinement.input.xray_data.r_free_flags { lattice_symmetry_max_delta=5 use_lattice_symmetry=True } ?

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Industrial Biostructures America 2018 conference
by Leonard,Paul G 20 Feb '18

20 Feb '18

Dear all, The inaugural Industrial Biostructures America conference will be held on 20-22 May 2018 at the Hilton La Jolla Torrey Pines Hotel in San Diego, California. Conference registration and accommodation information is available at: https://industrialbiostructuresamerica.org/ This conference brings together structural biologists from across the pharmaceutical and biotech industry to showcase their cutting-edge research. Scientific sessions will cover the following topics: * Cryo-EM * X-ray crystallography * Lead discovery using NMR * Protein design * Membrane crystallography The Abstract submission deadline is 23rd March 2018. We look forward to seeing you there, Paul Leonard Institute Research Scientist MD Anderson Cancer Center pleonard1(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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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Salbego, Cyndi 18 Feb '18

18 Feb '18

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. We currently have a number of days open in March. Below is a brief description of our beam lines, and links with more information. The 24-ID-C beamline can deliver X-rays in the range of 6 to 21 keV or ~2.1 to 0.5 Å. This covers most of the popular elemental edges for phasing. This wide energy-range also makes the beamline well suited for ultra high-resolution data collection and soft X-ray sulfur SAD phasing. The beamline is equipped with an optional kappa goniometer for optimal alignment of crystals. A Pixel Array Detector (PAD), Pilatus-6MF, installed on the 24-ID-C beamline helps measure very weak Bragg reflection intensities due to its noise-less readout technology and also provides a very fast data collection capability in shutter-less data collection mode. The 24-ID-E beamline is a fixed energy microdiffraction beamline delivering X-rays at 12.66 keV, optimized for Se-SAD experiments. It is equipped with an Eiger-16M Pixel Array Detector, offering advantages similar to those of the Pilatus-6MF. For more information on our beamlines (beamline and robot manuals): http://necat.chem.cornell.edu To ask about available time please contact Raj Rajashankar (rajashankar(a)anl.gov<mailto:[email protected]>) or Cyndi Salbego (csalbego(a)anl.gov<mailto:[email protected]>) for further information. To apply for General User Time (Rapid Access for current run cycle) please follow this link: https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page Cyndi Salbego Administrator, NECAT 630.252.0689

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9th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 14 Feb '18

14 Feb '18

First announcement 9th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 11 - June 15, 2018 Detailed information: https://conference.sns.gov/biologyneutrons18/ Application deadline: April 30, 2018 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Scattering Scientist, Neutron Sciences Directorate Oak Ridge National Laboratory

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Postdoctoral position in membrane protein structure and function at the NIH
by Anirban Banerjee 12 Feb '18

12 Feb '18

There is an open postdoctoral position for a membrane protein structure-function project in my lab at the NIH. We are currently focusing on integral membrane enzymes (Science. 2018, doi: 10.1126/science.aao6326) and transporters of transition metal ions (J Biol Chem. 2018, doi: 10.1074/jbc.M117.817478). Here is the formal announcement - EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT, BETHESDA, MD AND SURROUNDING AREA Position Description: The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We combine structural techniques such as macromolecular crystallography with biophysical and biochemical methods such as reconstitution based assays, high resolution microscopy and small molecule screening to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. Our laboratory is part of the Cell Biology and Neurobiology Branch in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). We also have an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). Qualifications: The candidates should hold a Ph. D. degree, be author of at least one first author publication and have a strong background in biochemistry or structural biology. Experience with basic molecular biology, protein expression, purification and biochemical characterization are required. Prior experience in membrane protein biochemistry or mammalian expression system for protein purification will be added advantages. It is absolutely essential the candidate is motivated and prepared to put in the best efforts for fruition of the project goals. We are a small, friendly lab and ability to work as part of a cohesive group is important. To Apply: Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests. The NIH is dedicated to building a diverse community in its training and employment programs.

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how to inhibit selectively undue H....O repulsion during refinement with phenix.refine ?
by Maxime Cuypers 10 Feb '18

10 Feb '18

Hello, i am refining neutron data with hydrogens on water molecules complexes that systematically bounce the whole molecule away from the hydroxyls or carboxylic groups or other waters. the Fo-Fc map is crystal clear about where the H atoms should go... any commands i can enter in i.e. a .param file to inhibit repulsion and promote closer h bonds? thanks for your help, cheers, Dr. Maxime Cuypers Post-Doctoral Research Associate, Structural Biology St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA

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query re local grid search in phenix.real_space_refine
by Oliver Clarke 10 Feb '18

10 Feb '18

Hi all, Related to the last message - when using local_grid_search, does phenix attempt to torsion-angle search every residue, or just outliers? It would seem like maybe using EMRinger or similar to identify residues where there is strong sidechain density, but in a non-rotameric position or with an incorrectly fit rotamer might be one way to make it more efficient if it is the former. I don’t want phenix trying to do a local grid search on residues with no sidechain density - these may be in an area of the map with poor local resolution, perhaps where I have docked a crystal structure, or carefully manually adjusted rotamers - local grid search in these regions is likely to make things worse if it is not focused on residues with clear sidechain density. Cheers Oli

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parallelization of local_grid_search in phenix.real_space_refine?
by Oliver Clarke 10 Feb '18

10 Feb '18

Hi all, phenix.real_space_refine runs pretty decently with run=minimization_global+adp, and the adp part is already parallelized. Using local_grid_search though, it slows down enormously, particularly for large structures, and I’d really like to try using it to correct poorly fit rotamers. Is there any prospect for parallelizing this function? Naively it seems like something that might be amenable to parallelization - so long as adjacent local grids aren’t searched at the same time, it would seem like one might be able to split up the job to run on multiple threads? These days a lot of folks have GPU workstations for cryoEM, which often (in addition to GPUs) have Xeon or Threadripper CPUs with many cores - I’d love to be able to use that computational horsepower effectively for refining my structures. Cheers Oli

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Phenix.molprobity PDB pre-test
by Rune Thomas Kidmose 09 Feb '18

09 Feb '18

Hi, After using Phenix.molprobity I noticed it does a test of the input PDB file in the beginning, where it, among other things, identifies duplicate atom labels and then proceeds to list some of them (and hides the rest some where I guess). It also identifies mismatches between the atom label and the atom type, e.g. if a CB is by mistake listed as an O instead of a C, in the last column in the PDB file. I would like to know if it is possible to somehow call this PDB pre-test function used within phenix.molprobity? or maybe something similar in the phenix package? I would like to use the feature in a small MD pipeline I am developing where the input PDB files are checked for duplicate atoms and mismatches between atom label and type. I believe something like the mentioned pre-test feature would work much better, than my current bash script solutions using combinations of awk, grep, sort, uniq etc. Cheers Ruki

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clashscore
by 潘晓伟 09 Feb '18

09 Feb '18

Hello everyone I refine a cryo EM data with 3.1 angstrom, the model fit well with the map, but the clashscore is high, abot 23. How can I decrease the value of clashscore with realspace.refinement in Phenix GUI. Thanks! Pan ________________________________ xiaowp82(a)hotmail.com

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