- phenixbb - phenix-online.org

model shifts after real space refinement
by Ashok Nayak 16 Dec '21

16 Dec '21

Hi, Is there a way to say keep_origin=False in phenix real space refinement. I used it in the command line version of v3958. It didn't take that. There is a model shift after the refinement which I think is because the program brings the map to the origin and hence the refined model as well. Thanks, Ashok -- Post-Doctoral Fellow Department of Biochemistry and Molecular Biology, Sidney Kimmel cancer Center Thomas Jefferson University 1020 Locust Street, JAH Philadelphia, PA, 19107 Phone: 804-661-4620

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Job Opportunities at Surrozen Inc (SFO Bay Area)
by Parthasarathy Sampathkumar 15 Dec '21

15 Dec '21

Dear All, I would like to bring to the attention of suitable candidates the following exciting job opportunities at Surrozen Inc, located in South San Francisco. Surrozen is a biotechnology company focused on discovering and developing novel regenerative medicines with a focus on unlocking the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway. Our vision is to engage the body’s own biological tissue repair mechanisms with our targeted regenerative antibodies, overcoming research and development hurdles that have been previously intractable, and have held back drug development efforts in the promising area of Wnt biology. *Research Associate/Senior Research Associate, Biochemistry and Biophysics:* https://apply.workable.com/surrozen/j/ACBA0B0D96/ *Scientist, Protein Sciences: * https://apply.workable.com/surrozen/j/DF4518083F/ *Research Associate, Protein Purification:* https://apply.workable.com/surrozen/j/7D64A01556/ Many Thanks, Best Wishes, Partha Sampathkumar PhD Principal Scientist Surrozen Inc Email: partha(a)surrozen.com

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NIH-funded Postdoc, Membrane Protein Structural Biology
by Alex Vecchio 14 Dec '21

14 Dec '21

Dear Phenix Community, I would like to bring your attention to an NIH-funded Postdoc position in the Vecchio Lab <https://vecchio-lab.unl.edu> at the University of Nebraska studying membrane proteins and membrane protein assemblies using X-ray crystallography and cryoEM. We are looking for a Ph.D., with experience in membrane proteins and/or crystallography. Potential exists for the candidate to *acquire cryoEM expertise* during the postdoc training via an NSF fellowship. For more information, please read our ad HERE <https://jobrxiv.org/job/vecchio-lab-at-university-of-nebraska-27778-nih-fun…> . To apply or for specific questions, please contact me at avecchio(a)unl.edu. All the best, Alex -- *Alex J. Vecchio, Ph.D.* *Assistant Professor* *University of Nebraska–Lincoln* *Department of Biochemistry* *Center for Integrated Biomolecular Communication* 1901 Vine Street N113 / N114 Beadle Center [Lab / Office] Lincoln, NE 68588 avecchio(a)unl.edu 1 [402] 472-2933

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Ligand CIF file in real space refinement
by Fadini, Alisia 06 Dec '21

06 Dec '21

Hello, I am trying to use phenix.real_space_refine to improve the fit between my protein's ligand and the electron density. I include a CIF file that has worked well for reciprocal space refinement, made through JLigand. It seems to me that the CIF file is read properly, it does not produce errors and the restrains are stated correctly in the output .cif file that includes all protein + ligand atoms. However, the output pdb shows a distorted ligand, where specific bond angles and bond lengths have been modified past what should be allowed by the restrains. Any insights on how to improve/the causes of this effect would be very welcome! My command is : phenix.real_space_refine model.pdb map.ccp4 ligand.cif resolution=1.63 Thank you, Alisia

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phenix installation problem
by princeadam＠163.com 04 Dec '21

04 Dec '21

Dear all I tried to install Phenix on my virtual machine(Ubuntu) in win11. And got the following error message. ========================================================================== Phenix Installation version: 1.19.2-4158 machine type: intel-linux-2.6-x86_64 OS version: 5.11.0-40-generic destination: /usr/local/phenix-1.19.2-4158 # of processors: 1 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 245, in <module> installer(sys.argv[1:]).install() File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 200, in install self.install_from_binary() File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 349, in install_from_binary self.reconfigure(log=log) File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 431, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 55, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-1.19.2-4158/conda_base/bin/python /usr/local/phenix-1.19.2-4158/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.19.2-4158/build --command_version_suffix 1.19.2-4158 phenix phaser solve_resolve labelit dials xia2 iota prime amber_adaptbx --use_conda' failed with exit code 127 I searched phenixbb, and got the similar information from http://www.phenix-online.org/pipermail/phenixbb/2015-November/022456.html It's a pity , that the answer was not suiable for me. I have root access to write to usr/local. And under /usr/local/phenix-1.19.2-4158 , I can see four folders:build, conda_base, doc, modules. Any one has suggestions? all the best Adam

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opportunity for experienced crystallographer
by Mooers, Blaine H.M. (HSC) 30 Nov '21

30 Nov '21

Associate Director of the Laboratory of Biomolecular Structure and Function The Laboratory of Biomolecular Structure and Function (LBSF) at the University of Oklahoma Health Sciences Center (OUHSC) seeks an experienced crystallographer to run the daily operations of the LBSF. The position is at the Assistant Professor of Research level. The candidate will be responsible for working with PIs to advance their structural biology projects. These efforts will include routine technical operations, developing new protocols to overcome challenging problems, and training the staff of user labs in protein purification, crystallization, data collection, and structure determination. The ideal candidate for this position will have a PhD and ten years of experience in macromolecular crystallography. The candidate will not be expected to write grant applications. Pluses in a candidate's background include experience with membrane protein purification and LCP crystallization, experience with Cyro-EM, or experience with other structural biology methods like microED, SAXS, SANS, XAFS, NMR, or XFELS. The LBSF is part of a suite of core labs supported in part by the OUHSC Vice President of Research. The LBSF is also part of the Biomolecular Structure Core (BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural Biology (OCSB), which is based on the main campus in Norman. The BSC has contributed to the awarding of 23 million dollars in grant funding and 33 publications in the past nine years. The OCSB has been the focal point of Oklahoma's structural biology community for nine years. The community includes 50 labs at three major research institutions. The BSC will be a vital part of a new Center for Therapeutic Science. The center will coordinate and foster the drug development pipeline with the BSC playing a central role in structure-based drug design. The LBSF will be working closely with Dr. Matt Hart (https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/hart-matthew-phd-1), Director of the newly established Center for High Throughput Screening. Most of the 12 major users of the LBSF have cancer-related projects. One project led to the 2021 publication of crystal structures of RET Kinase bound to two drug molecules recently approved by the FDA for the treatment of non-small cell lung cancer. Most of the major users are members of the Stephenson Cancer Center, a National Cancer Institute-designated cancer center. The compensation level for this full-time position includes a generous benefits package. The position is based in Oklahoma City -- an affordable place to raise a family. To apply, please submit a cover letter, CV and contact information (name and email) for three references to Blaine Mooers, Director of the Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at http://ouhsc.edu. The position will remain open until filled. Application review will begin immediately. OUHSC is an equal opportunity employer and is committed to creating a diverse and inclusive environment for all employees. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Struc… COBRE in Structural Biology: https://www.ou.edu/structuralbiology

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iotbx.merging_statistics on Python 3: too memory consuming
by Martin Malý 29 Nov '21

29 Nov '21

Dear PHENIX & CCTBX developers and users, I tried to calculate merging statistics with CCTBX tools using Python 3. I realized that the memory requirements are much higher comparing with Python 2... I closed all programs firstly so I had just 1.6 GB RAM used of 7.6 GB total RAM. Then I ran these two lines of code in the cctbx.python shell: import iotbx.merging_statistics i_obs = iotbx.merging_statistics.select_data(file_name="XDS_ASCII.HKL", data_labels=None) Python 2.7: The RAM usage went to 4.8 GB and then I was able to calculate merging statistics. Python 3.7: The module import was successful. Then the RAM usage went to total 7.6 GB and then the process was killed by the operating system (CentOS 7). Please, do you have any suggestion how to use this module "more carefully" and save memory? Thank you! Best regards, Martin Malý ----- Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences.

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Job vacancy: Institute Research Investigator within the Therapeutics Discovery Division at MD Anderson Cancer Center
by Leonard,Paul G 18 Nov '21

18 Nov '21

Hi, The Structural Chemistry group, within the Therapeutics Discovery Division of MD Anderson Cancer Center is looking for a highly motivated individual with a strong background in structural biology, using X-ray crystallography and/or single particle cryo-EM to determine high resolution structures of proteins and protein complexes. Our mission is to integrate novel biological insights with drug discovery expertise to accelerate the development of innovative, targeted, small-molecule therapeutics for the treatment of cancer or neurodegenerative diseases. Our work is conducted in a team science environment that brings together excellence in both academic and pharmaceutical discovery. The structural chemistry group provides structural biology support for several drug discovery programs in our pipeline, spanning from early stage drug discovery through lead optimization. For a full job description and to submit an application please use the following link... https://jobs.mdanderson.org/search/jobdetails/institute-research-investigat… kind regards, Paul Leonard Senior Institute Research Scientist MD Anderson Cancer Center 1881 East Road Houston TX 77054 USA 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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Research Associate position in structural biology at Takeda in San Diego
by L Qin 18 Nov '21

18 Nov '21

Dear PHENIX user mailing list members, The Structural Biology group at Takeda Pharmaceuticals in San Diego California has an open position for a Research Associate. I invite interested candidates to apply through the following link: https://www.takedajobs.com/job/san-diego/research-associate-structural-biol… Please feel free to contact me for further information. Best regards, Ling Ling Qin PhD Structural Biology Takeda Development Center Americas 9625 Towne Centre Dr, San Diego, CA 92121 <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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MizzouForward faculty hiring campaign
by Tanner, John J. 17 Nov '21

17 Nov '21

Dear Colleagues: The University of Missouri has initiated a major faculty hiring campaign, called MizzouForward, which intends to hire 150 new faculty members over the next 5 years. Successful candidates must be research leaders with a passion for collaboration and a proven track record of active, external research funding, particularly from federal agencies like NIH. This initiative coincides with the recent grand opening of the NextGen Precision Health research building, which houses a newly upgraded imaging center with a Krios G4 and Aquilos Cryo-FIB. Other investments in structural biology include a share of ALS beamline 4.2.2 and a Bruker 800 MHz NMR with cryoprobe. For more information, please see: https://provost.missouri.edu/mizzou-forward/ -- Jack Tanner (tannerjj(a)missouri.edu<mailto:[email protected]>) and Lesa Beamer (BeamerL(a)missouri.edu<mailto:[email protected]>) Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211

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Low resolution refinement
by Armando Albert 17 Nov '21

17 Nov '21

Dear all, I have got a very promising MR solution at 5A resolution. Can I refine this structure? Any hint would be very much appreciated Armando

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RapiData 2020 applications open
by Smith, Clyde 16 Nov '21

16 Nov '21

Applications are now open for the 2020 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held in sunny California at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from March 30 - April 4 2020. Course organizers for 2020 are Silvia Russi, Clyde Smith and Jeney Wierman. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, Data collection strategies, X-ray light sources, X-ray detectors, Data reduction, Structure solution by MAD, SAD and Molecular Replacement, Complementary methods (spectroscopy and small angle scattering). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. The application deadline is November 10 2019. Successful applicants will be notified shortly thereafter, and invited to register and book accommodation at the SLAC Guesthouse at that time. A limited amount of travel support funding may be available. Please direct questions to Silvia Russi (srussi(a)slac.stanford.edu), Jeney Wierman (jwierman(a)slac.stanford.edu) or Clyde Smith (csmith(a)slac.stanford.edu).

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Thresholding for N/Q/H errors in phenix.refine?
by Nicholas Gao 15 Nov '21

15 Nov '21

Hi, For the correction of N/Q/H errors in phenix.refine: is this option binary (that is, can it only be turned on or off)? Or can it be adjusted to be on but its stringency adjusted to an arbitrary scale? https://phenix-online.org/documentation/reference/refinement.html#id19 <--suggests its binary, but asking here for thoroughness. Sincerely, Nicholas Gao

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superpose mrc maps (and also mtz files)
by Georg Mlynek 15 Nov '21

15 Nov '21

Dear Scientific community, I got a few .mrc maps from collaborators. Is there a way in phenix to superpose models and corresponding mrc maps. Using superpose maps I get the error:" This file format CCP4 map is not supported as input for this field; only files of type 'Reflections' are allowed. Also the program Structure comparison does not recognize .mrc files. On top there are also a few mtz files I would like to superpose on the .mrc files. Many thanks, br Georg.

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Phenix bug report [[email protected] - Mon Jun 22 19:42:79 2021]
by Robert Munoz 15 Nov '21

15 Nov '21

User name: Robert Munoz E-mail address: robertm(a)lbl.gov Version: 1.18.2-3874 Platform: mac-intel-osx-x86_64 Comments: Trying to refinement using locscale out map Traceback: RuntimeError : cctbx Internal Error: /Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64/modules/cctbx_project/cctbx/maptbx/resolution.h(38): CCTBX_ASSERT(sum_all != 0.) failure. Traceback: File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/libtbx/runtime_utils.py", line 181, in run return_value = self.target() File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/libtbx/runtime_utils.py", line 76, in __call__ result = self.run() File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 908, in run self.result = run(args=self.args, validated=True, log=sys.stdout) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 581, in __init__ self.caller(func = self.initialize, prefix="Initialize") File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 619, in caller status = func(prefix=prefix, **kwargs) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 696, in initialize self.inputs = self.process_inputs() File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 675, in process_inputs return process_inputs_stage_1(process_inputs_stage_0_object=pis_0, log=self.log) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 403, in process_inputs_stage_1 crystal_symmetry = model.crystal_symmetry()).result.d99 File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/cctbx/maptbx/__init__.py", line 117, in __init__ d_max = self.d_max) Platform info: __FILE__ = /Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64/modules/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = May 17 2020 __TIME__ = 22:35:27 __TIMESTAMP__ = Thu Feb 27 10:57:04 2020 __x86_64__ __APPLE_CC__ = 6000 __GNUC__ = 4 __GNUC_MINOR__ = 2 __GNUC_PATCHLEVEL__ = 1 __clang__ __clang_major__ = 11 __clang_minor__ = 0 __clang_patchlevel__ = 0 __clang_version__ = 11.0.0 (clang-1100.0.33.17) __llvm__ __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 4.2.1 Compatible Apple LLVM 11.0.0 (clang-1100.0.33.17) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 63 __SSE2__ = 1 BOOST_LIB_VERSION = 1_63 PY_VERSION = 2.7.15 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG boost/TAG: None os.name: posix sys.platform: darwin sys.byteorder: little platform.platform(): Darwin-17.7.0-x86_64-i386-64bit platform.architecture(): ('64bit', '') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 4 Memory total: 17,179,869,184 Memory free: unknown import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å

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Double difference anomalous maps
by Mark Saper 10 Nov '21

10 Nov '21

I tried the "Isomorphous difference map” action and specified a file for input 1 containing F1+, F1– at one wavelength, and the file input 2 containing F2+,F2– at another wavelength. I selected the appropriate Labels for the columns containing the anomalous data. I then specified in "Advanced Options” to use anomalous differences instead of amplitudes. Will this procedure use the following coefficients for the difference Fourier? ( F1(+) – F1(–) ) – ( F2(+) – F2(–) ), alpha(calc) Can someone confirm if this is indeed what is calculated? Many thanks, Mark Saper __________________ Mark A. Saper, Ph.D. Visiting Professor at the Faculty of Medicine Hebrew University of Jerusalem Ein Kerem Jerusalem ISRAEL saper(a)umich.edu mobile +972 52 815-0480‬ Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

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Parameters in "reference_model" during "real space refinement"
by Coudray, Nicolas 09 Nov '21

09 Nov '21

Hi, I would be interested in understanding more the exact meaning of the options related to "reference model" when doing "real space refinement" (in https://phenix-online.org/documentation/reference/real_space_refine.html): * hydrogens = False * main_chain = True * side_chain = True * fix_outliers = True * strict_rotamer_matching = False * auto_shutoff_for_ncs = False * secondary_structure_only = False It is a bit unclear what setting each of them to "True" would exactly imply or what the difference between them are. Does anyone have more information? Thanks, Best, Nicolas ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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eLBOW crashes Phenix
by Xavier Brazzolotto 03 Nov '21

03 Nov '21

Hi, I am using the latest stable Phenix release (1.19.2-4158) on macOS (v12.0.1) and I do have an odd bug with Phenix eLBOW. The program by it self runs and generates the expected cif files. If I open REEL to check the models, I do see them but as soon as I exit REEL, it crashes the whole Phenix process. Is it a know bug ? I paste the crash report below if this helps. ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: python [57745] Path: /Applications/phenix-1.19.2-4158/*/python.app/Contents/MacOS/python Identifier: com.continuum.python Version: ??? Code Type: X86-64 (Native) Parent Process: launchd [1] User ID: 501 Date/Time: 2021-11-03 18:05:27.1449 +0100 OS Version: macOS 12.0.1 (21A559) Report Version: 12 Bridge OS Version: 6.0 (19P548) Anonymous UUID: 461A1FA5-1FFE-CC49-2057-0C0BB25A7143 Sleep/Wake UUID: 335CBE5C-1D37-4713-B3EA-80B0E830794F Time Awake Since Boot: 300000 seconds Time Since Wake: 13706 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000020 Exception Codes: 0x0000000000000001, 0x0000000000000020 Exception Note: EXC_CORPSE_NOTIFY Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [57745] VM Region Info: 0x20 is not in any region. Bytes before following region: 4480602080 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL UNUSED SPACE AT START ---> __TEXT 10b109000-10b10a000 [ 4K] r-x/rwx SM=COW .../MacOS/python Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libobjc.A.dylib 0x7ff81e00bc4f objc_release + 31 1 Foundation 0x7ff81f1ecde8 empty + 58 2 Foundation 0x7ff81f094dd9 dealloc + 38 3 Foundation 0x7ff81f094d64 -[NSConcreteMapTable dealloc] + 54 4 libobjc.A.dylib 0x7ff81e0290fe objc_object::sidetable_release(bool, bool) + 232 5 AppKit 0x7ff8212d8c4c ___NSTouchBarFinderSetNeedsUpdateOnMain_block_invoke_2 + 2233 6 AppKit 0x7ff820d3130c NSDisplayCycleObserverInvoke + 155 7 AppKit 0x7ff820d30e97 NSDisplayCycleFlush + 952 8 QuartzCore 0x7ff8252a5434 CA::Transaction::run_commit_handlers(CATransactionPhase) + 98 9 QuartzCore 0x7ff8252a41b2 CA::Transaction::commit() + 376 10 AppKit 0x7ff820dd24e2 __62+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayLink]_block_invoke + 285 11 AppKit 0x7ff821518724 ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 12 CoreFoundation 0x7ff81e23bc07 __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 23 13 CoreFoundation 0x7ff81e23baa4 __CFRunLoopDoObservers + 543 14 CoreFoundation 0x7ff81e23af37 __CFRunLoopRun + 841 15 CoreFoundation 0x7ff81e23a52d CFRunLoopRunSpecific + 563 16 HIToolbox 0x7ff826e583e1 RunCurrentEventLoopInMode + 292 17 HIToolbox 0x7ff826e58008 ReceiveNextEventCommon + 284 18 HIToolbox 0x7ff826e57ed5 _BlockUntilNextEventMatchingListInModeWithFilter + 70 19 AppKit 0x7ff820c658f0 _DPSNextEvent + 886 20 AppKit 0x7ff820c63f5c -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1411 21 AppKit 0x7ff820c56359 -[NSApplication run] + 586 22 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d2b0a23 wxGUIEventLoop::OSXDoRun() + 115 23 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d192ce4 wxCFEventLoop::DoRun() + 52 24 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d0c2885 wxEventLoopBase::Run() + 165 25 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d087521 wxAppConsoleBase::MainLoop() + 209 26 _core_.so 0x10bd94114 wxPyApp::MainLoop() + 84 27 _core_.so 0x10bdf7902 _wrap_PyApp_MainLoop(_object*, _object*) + 82 28 libpython2.7.dylib 0x10b4967ee PyEval_EvalFrameEx + 30382 29 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 30 libpython2.7.dylib 0x10b409a84 function_call + 388 31 libpython2.7.dylib 0x10b3dcce1 PyObject_Call + 97 32 libpython2.7.dylib 0x10b3ee5d4 instancemethod_call + 180 33 libpython2.7.dylib 0x10b3dcce1 PyObject_Call + 97 34 libpython2.7.dylib 0x10b4957b6 PyEval_EvalFrameEx + 26230 35 libpython2.7.dylib 0x10b49c631 fast_function + 337 36 libpython2.7.dylib 0x10b495889 PyEval_EvalFrameEx + 26441 37 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 38 libpython2.7.dylib 0x10b49c54a fast_function + 106 39 libpython2.7.dylib 0x10b495889 PyEval_EvalFrameEx + 26441 40 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 41 libpython2.7.dylib 0x10b48e642 PyEval_EvalCode + 34 42 libpython2.7.dylib 0x10b4c0901 PyRun_FileExFlags + 161 43 libpython2.7.dylib 0x10b4c035f PyRun_SimpleFileExFlags + 847 44 libpython2.7.dylib 0x10b4d8dfb Py_Main + 3483 45 dyld 0x11609f4fe start + 462 Thread 1:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x7ff81e138aba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x7ff81e138e2b mach_msg + 59 2 CoreFoundation 0x7ff81e23ca42 __CFRunLoopServiceMachPort + 319 3 CoreFoundation 0x7ff81e23b11b __CFRunLoopRun + 1325 4 CoreFoundation 0x7ff81e23a52d CFRunLoopRunSpecific + 563 5 AppKit 0x7ff820dd3cec _NSEventThread + 132 6 libsystem_pthread.dylib 0x7ff81e175514 _pthread_start + 125 7 libsystem_pthread.dylib 0x7ff81e17102f thread_start + 15 Thread 2: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 3: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 4:: Dispatch queue: com.apple.NSXPCConnection.user.endpoint.NSRemoteView.IMKTextInputFunctionRowItemServiceViewController 0 CoreFoundation 0x7ff81e1c5746 CFHash + 134 1 CoreFoundation 0x7ff81e1e49fb CFBasicHashAddValue + 223 2 CoreFoundation 0x7ff81e22e09c CFSetCreate + 66 3 CoreFoundation 0x7ff81e223179 CFRunLoopPerformBlock + 288 4 ViewBridge 0x7ff82572020d deferBlockOntoMainThread + 280 5 ViewBridge 0x7ff82572d4d5 deferNSXPCInvocationOntoMainThread + 130 6 Foundation 0x7ff81f0acc12 -[NSXPCConnection _decodeAndInvokeMessageWithEvent:flags:] + 1576 7 Foundation 0x7ff81f063f1a message_handler + 206 8 libxpc.dylib 0x7ff81deba530 _xpc_connection_call_event_handler + 56 9 libxpc.dylib 0x7ff81deb928c _xpc_connection_mach_event + 1387 10 libdispatch.dylib 0x7ff81dfbed63 _dispatch_client_callout4 + 9 11 libdispatch.dylib 0x7ff81dfd78b7 _dispatch_mach_msg_invoke + 452 12 libdispatch.dylib 0x7ff81dfc4b85 _dispatch_lane_serial_drain + 335 13 libdispatch.dylib 0x7ff81dfd83fb _dispatch_mach_invoke + 484 14 libdispatch.dylib 0x7ff81dfc4b85 _dispatch_lane_serial_drain + 335 15 libdispatch.dylib 0x7ff81dfc57c8 _dispatch_lane_invoke + 366 16 libdispatch.dylib 0x7ff81dfcf7e1 _dispatch_workloop_worker_thread + 758 17 libsystem_pthread.dylib 0x7ff81e17208f _pthread_wqthread + 326 18 libsystem_pthread.dylib 0x7ff81e17101b start_wqthread + 15 Thread 5: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 6: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 7: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 8: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 9: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 10: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 11: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 12: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x6000000000000000 rbx: 0x0000000000000018 rcx: 0x0000000000000000 rdx: 0x00007f8ec5973a00 rdi: 0x00007f8ea57830d0 rsi: 0x0000000000000000 rbp: 0x00007ff7b4df3260 rsp: 0x00007ff7b4df3238 r8: 0x0000000000000200 r9: 0x00007f8ec5972d20 r10: 0x00007ff85f8105d0 r11: 0x00007ff81f094d2e r12: 0x00007f8f01f8e7c0 r13: 0x00007ff85f966a01 r14: 0x00007f8f01f8e7c8 r15: 0x000000000000000d rip: 0x00007ff81e00bc4f rfl: 0x0000000000010246 cr2: 0x0000000000000020 Logical CPU: 0 Error Code: 0x00000004 (no mapping for user data read) Trap Number: 14 Thread 0 instruction stream: 34 48 89 c2 48 01 ca 72-12 f0 48 0f b1 17 74 25 4H..H..r..H...t% a8 01 75 e4 31 f6 e9 7c-d7 01 00 31 f6 e9 eb 86 ..u.1..|...1.... 00 00 48 b9 f8 ff ff ff-ff 7f 00 00 48 21 c8 f6 ..H.........H!.. 40 1c 01 74 df 48 89 f8-c3 90 90 90 90 90 90 90 @..t.H.......... 90 48 85 ff 74 76 89 f8-83 e0 01 48 85 c0 75 6c .H..tv.....H..ul 48 8b 07 48 b9 f8 ff ff-ff ff 7f 00 00 48 21 c1 H..H.........H!. [48]8b 51 20 f6 c2 04 74-54 a8 01 74 6f 48 b9 00 H.Q ...tT..toH.. <== 00 00 00 00 00 80 00 48-ba 00 00 00 00 00 00 00 .......H........ 01 48 39 c8 72 36 48 89-c6 48 29 d6 72 17 f0 48 .H9.r6H..H).r..H 0f b1 37 74 22 a8 01 75-e8 31 f6 ba 01 00 00 00 ..7t"..u.1...... e9 82 d3 01 00 48 85 c8-75 3a 48 8b 35 18 f5 99 .....H..u:H.5... 41 ff 25 f2 d2 e6 3f 48-39 ce 72 ee c3 f6 c2 02 A.%...?H9.r..... 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(*) <00000000-0000-0000-0000-000000000000> ??? External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%) Writable regions: Total=2.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.6G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 896K 7 Activity Tracing 256K 1 CG backing stores 2528K 4 CG image 1596K 41 CG raster data 184K 21 ColorSync 228K 26 CoreAnimation 139.5M 206 CoreGraphics 12K 2 CoreImage 608K 35 CoreUI image data 2480K 21 Foundation 80K 2 Kernel Alloc Once 8K 1 MALLOC 511.7M 149 MALLOC guard page 48K 9 MALLOC_MEDIUM (reserved) 880.0M 8 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) STACK GUARD 56.0M 13 Stack 14.1M 13 VM_ALLOCATE 1128K 27 VM_ALLOCATE (reserved) 768.0M 1 reserved VM address space (unallocated) __DATA 41.4M 510 __DATA_CONST 23.2M 234 __DATA_DIRTY 969K 139 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 682.2M 110 __OBJC_RO 81.5M 1 __OBJC_RW 3120K 2 __TEXT 529.9M 498 __UNICODE 588K 1 dyld private memory 3072K 3 mapped file 158.3M 26 shared memory 1296K 19 =========== ======= ======= TOTAL 4.2G 2133 TOTAL, minus reserved VM space 2.2G 2133 ----------- Full Report ----------- {"app_name":"python","timestamp":"2021-11-03 18:05:27.00 +0100","app_version":"","slice_uuid":"41b01d14-4c6e-3a14-a84e-812c0ee8d9cd","build_version":"","platform":1,"bundleID":"com.continuum.python","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.0.1 (21A559)","incident_id":"3B71C390-9A85-4125-A53A-7058CF9E1361","name":"python"} { "uptime" : 300000, "procLaunch" : "2021-11-03 18:04:29.4653 +0100", "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "MacBookPro15,1", "procStartAbsTime" : 303473294854732, "coalitionID" : 1512, "osVersion" : { "train" : "macOS 12.0.1", "build" : "21A559", "releaseType" : "User" }, "captureTime" : "2021-11-03 18:05:27.1449 +0100", "incident" : "3B71C390-9A85-4125-A53A-7058CF9E1361", "bug_type" : "309", "pid" : 57745, "procExitAbsTime" : 303530973462636, "cpuType" : "X86-64", "procName" : "python", "procPath" : "\/Applications\/phenix-1.19.2-4158\/*\/python.app\/Contents\/MacOS\/python", "bundleInfo" : {"CFBundleIdentifier":"com.continuum.python"}, "storeInfo" : {"deviceIdentifierForVendor":"4FD8A66E-22D2-5A3D-904B-4E69B0B05DAE","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "org.pythonmac.unspecified.phenix-1.19.2-4158", "crashReporterKey" : "461A1FA5-1FFE-CC49-2057-0C0BB25A7143", "responsiblePid" : 57744, "wakeTime" : 13706, "bridgeVersion" : {"build":"19P548","train":"6.0"}, "sleepWakeUUID" : "335CBE5C-1D37-4713-B3EA-80B0E830794F", "sip" : "enabled", "vmRegionInfo" : "0x20 is not in any region. 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Phenix 1.20 release candidates
by Billy Poon 02 Nov '21

02 Nov '21

Hi everyone, We are doing a final Python 2.7 release of Phenix and the first release candidate is available from https://phenix-online.org/download/nightly_builds.cgi This release will contain several new features, such as tools for using AlphaFold models. The release after that is planned to be in Python 3.7. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 27 Oct '21

27 Oct '21

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 DEC 2021. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template is attached to this email. 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 ORCID : orcid.org/0000-0001-8857-9464

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Re: [phenixbb] Restricting real-space refinement and weights to specific atom selections
by Josh Cofsky 20 Oct '21

20 Oct '21

Thanks for that suggestion, Phil. After several weeks, I've finally found solid answers to all my questions, which I'll write here in case anyone reading this message is curious: Q1: Is there any way to apply different map weights to different pieces of the structure during refinement? A1: Pavel tells me the answer is no—this feature is not available in Phenix yet. The way I was able to accomplish something to a similar effect was by performing full-model refinements at different weights. Then, in a final refinement job, use torsion restraints from each of those output models (as reference models) across the desired stretches of residues. Clunky, but it solved a few problems for me. Q2: How is the generic "weight" parameter at the bottom of the Phenix GUI applied to the refinement? A2: The target function is T = Tmap * weight + Trestraints. At the time of writing this message, there is a typo in the Phenix Real-Space Refine documentation, which incorrectly reports the target function as "T = Tmap + weight * Trestraints" (Pavel confirmed). Q3: Why is the PDB validation telling me I have geometric issues that were not acknowledged by Phenix? A3: Phil is right. The ESD for several nucleic acid bond lengths and angles is wide as compared to the sigma tolerated by wwPDB. To fix this, I went into the CIF files within the geostd folder and made the following changes to the troublesome RNA and DNA nucleotide files: *data_AD.cif, data_TD.cif, data_CD.cif, data_GD.cif:* length: C1'-N1, ESD=0.020 C3'-O3', ESD=0.020 angles: O4'-C1'-N9/N1, ESD=0.30 *data_U.cif* angles: C5-C6-N1, ESD=0.5 C6-N1-C2, ESD=0.5 *data_C.cif* angles: C6-N1-C2, ESD=0.5 *data_A.cif* angles: N7-C8-N9, ESD=0.5 Best, Josh On Mon, Sep 13, 2021 at 7:23 AM Philip D. Jeffrey <pjeffrey(a)princeton.edu> wrote: > :: most of the outliers are not acknowledged as such (by Phenix), and I > only become > :: aware of them when the wwPDB validation tells me they are there. > > Check that the equilibrium values that PDB are using and the ones that > Phenix are using are the same. If they're not (or if the sigmas are way > different) you're not going to be able to change the outcome just by > changing weights. > > Phil Jeffrey > Princeton > > ------------------------------ > *From:* phenixbb-bounces(a)phenix-online.org < > phenixbb-bounces(a)phenix-online.org> on behalf of Josh Cofsky < > josh.cofsky(a)gmail.com> > *Sent:* Sunday, September 12, 2021 9:42 PM > *To:* phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> > *Subject:* Re: [phenixbb] Restricting real-space refinement and weights > to specific atom selections > > I now realize that I am confused as to what the mentioned "weight" > parameter refers to. The Phenix RSR documentation contains a line that > reads "T = Tmap + weight * Trestraints"—if I'm understanding correctly > (?), this means a larger "weight" value should yield greater conformity to > geometric restraints at the expense of model/map fit. In reality, I observe > the opposite trend in my refinements (which is why I assumed it was a "map > weight"). Can someone clarify what "weight" (Refinement Settings > "Other > Options") refers to? > > The reason I am exploring these questions is that Phenix RSR is > introducing bond angle outliers into a low-resolution area of a DNA > molecule in my model—most of the outliers are not acknowledged as such (by > Phenix), and I only become aware of them when the wwPDB validation tells me > they are there. I assumed this was the result of overfitting to the map > because setting "weight" to 0.0 prevented these outliers from appearing, > but at the expense of map-model fit in the remainder of the structure > (which is why I wanted to apply different weights to different segments of > the model). > > Thanks, > Josh > > On Sun, Sep 12, 2021 at 12:21 PM Josh Cofsky <josh.cofsky(a)gmail.com> > wrote: > > Hi all, > > I'm using phenix.real_space_refine to refine a model into a cryo-EM map. > My local map resolution is highly variable across the molecule, and using a > single map weight (the parameter shown in the Refinement Settings > "Other > Options" in the GUI) on the whole model leads to poor map-to-model fit in > some locations and overfitting in others. Potential solutions could be to: > 1. assign different map weights to different segments of the model (based > on a user-specified atom selection) > OR > 2. perform iterative refinements with different weight settings, holding > different (user-specified) segments of the model fixed during each > iteration (I suspect this isn't possible based on Pavel's message here: > http://phenix-online.org/pipermail/phenixbb/2021-May/025037.html) > > Is either of these approaches (or another one that accomplishes the same > goal) possible? I am using the Phenix GUI, but if this is only possible in > command line, and you're willing to share an example command that > accomplishes either of these tasks, please let me know. > > Thanks! > -Josh > > (also, apologies if this is a duplicate message...still trying to figure > out the phenixbb listserv) > >

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Job opening: Scientist/Sr. Scientist, Structural Biology at Plexxikon Inc, South San Francisco, CA, USA
by Ying Zhang 16 Oct '21

16 Oct '21

Dear all, This post is to bring your attention to a job opportunity of a scientist/Sr. Sicentist position at Plexxikon Inc. We are looking for a highly motivated, structural biologist with expertise in crystallography. Plexxikon (https://www.plexxikon.com/) is located in South San Francisco at CA, USA. We only consider candidates based in US. This Scientist will be a critical member of the Structural Chemistry team. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. Plexxikon utilizes its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage compounds in a number of therapeutic areas, including two marketed drug. Zelboraf(tm) (vemurafenib) was the first precision medicine to be approved for the treatment of BRAF-mutant metastatic melanoma; Turalio(tm) (pexidartinib) was the first FDA-approved therapy for tenosynovial giant cell tumor. You can find details about this position at https://careers.jobscore.com/careers/plexxikon/jobs/scientist-structural-bi… Please apply through the link. Best Regards, Ying Zhang, Ph.D Sr Director, Research Planning Plexxikon Inc

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missing statistics for rama-z
by Hannah Bridges 16 Oct '21

16 Oct '21

Hello, I have a PDB for which, when I run either realspace refinement or validation, phenix does not show rama-z scores for helix or sheet (and the structure is not entirely loops..) Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.08), residues: 8101 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.06), residues: 8101 It seems peculiar to this one model, as other very similar ones are fine, but is this something that other people have seen before? I can supply the PBD off-list for investigation. Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

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Nightly build downloads
by Armando Albert 02 Oct '21

02 Oct '21

Dear all, I am unable to find the nightly build releases from the Phenix web page. Is there any issue I do not know? Armando

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Phenix website change complete
by Dorothee Liebschner 01 Oct '21

01 Oct '21

Hi everyone, We changed the website. Let us know if there are any issues. Best wishes, The Phenix Team -- Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Phenix website maintenance on 9/30/2021
by Dorothee Liebschner 30 Sep '21

30 Sep '21

Hi everyone, The Phenix website will be changed tomorrow, Thursday 9/30/2021. Therefore, the website might not be available for a couple of hours. If you encounter any problems after the switch - which we will announce on the BB - please let us know. We will change the urls of some pages due to some reorganization, but the addresses of the most visited pages should be the same, such as download, documentation and so on. Best wishes, The Phenix Team -- Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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problems with phenix.refine and wwPDB deposition
by Błażej Bagiński 24 Sep '21

24 Sep '21

Dear fellow Phenix bulletin boarders, I'd like to ask for help with refinement-deposition file conflict. I 'finished' solving the structure (protein, 1 chain, 2 ligands), doing the final refinement in phenix.refine. Structure looks okay and does not report any errors in phenix/coot. I than started the deposition with the wwPDB OneDep System.After long check, my files were rejected (multiple errors, with the best one being "coordinates not found"). Following the FAQ, I run the prepare_pdb_deposition, but the results were the same. I also tried using PDB_Extract (https://pdb-extract.wwpdb.org/), with its result file also generating plethora of errors. As a control, I put the same phenix.refine file into the PDB-REDO server, and its results finished wwPDB validation successfully. Trouble is, PDB-REDO is quite aggressive and messed up one ligand, occupancies and two loops, so I would prefer to not submit it for anyone to see. How do you make refinement output compatible with wwPDB? Is there a way to run PDB-REDO without the REDO? Kind regards, Blazej Baginski

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Download issues
by Billy Poon 24 Sep '21

24 Sep '21

Hi everyone, If you are having download issues, can you post a message here? We are seeing reports of download issues from some users and we want to determine how widespread the issue is. Some users have said that the download works after waiting for a bit or by using the incognito or private mode of their browser. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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Postdoctoral Research Opportunity in Cryo-EM at University of Washington, in Seattle, USA
by George Wisedchaisri 18 Sep '21

18 Sep '21

Hi, I have a job opening announcement for a joint postdoctoral position in the Catterall and Zheng Labs at University of Washington, in Seattle, WA, USA. Please see the link below for more detailed info. http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20210913/9614f6ba/att… Thanks, George Wisedchaisri -- *Postdoctoral Research Position* *Senior Fellow or Instructor Appointment Level* *Structural Basis for Function and Pharmacology of Voltage Gated Sodium and Calcium Channels* *Laboratories of William A. Catterall and Ning Zheng* *Department of Pharmacology, University of Washington, Seattle, WA 98195-7280 USA* *Please respond by e-mail to wcattlab(a)uw.edu <wcattlab(a)uw.edu> with Postdoctoral Application on the Subject Line* *Position Requirements* PhD or equivalent in biochemistry, biophysics, bioengineering, or structural biology. Experience in molecular biology, cell culture, and protein expression, purification, and characterization. Excellent communication skills and successful experience in a team research environment. Two years experience with cryo-EM data collection, processing, and analysis. Successful determination of a protein structure by cryo-EM. *Application Requirements* Curriculum Vitae Names of three referees *University of Washington is an affirmative action, equal opportunity employer. All qualified applicants will receive consideration without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, national origin, age, protected veteran or disabled status, or genetic information.* -- George Wisedchaisri, Ph.D. Research Assistant Professor of Pharmacology --------------------------------------------- University of Washington School of Medicine Department of Pharmacology 1959 NE Pacific St Seattle, WA 98195-7280

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Today is the last day to register for the SSRL/LCLS User Meeting
by Mooers, Blaine H.M. (HSC) 18 Sep '21

18 Sep '21

Dear Phenixbb: Today is the last day to register for the SSRL/LCLS User Meeting that starts on Monday. It is free and virtual. https://events.bizzabo.com/SLAC-UsersMeeting-2021/home. The poster session runs 12 - 1 PM Pacific Time M-Th. You use the gathertown software to attend it. Navigation of the poster session is like playing a 1990s computer game. I was on the poster judging team. We spent this week judging the posters virtually. We made our selections of the seven poster prize finalists today. All of the semifinalist posters were excellent. Best regards, Blaine SSRL UEC member and past chair. Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Struc… COBRE in Structural Biology: https://www.ou.edu/structuralbiology

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(no subject)
by Smita Yadav 17 Sep '21

17 Sep '21

Dear All, hello to everyone. I wanted to know which gromac version is mostly used for simulation in linux. -- With Regards Smita Yadav

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NIH-funded Postdoc, Membrane Protein Structural Biology (Nebraska, USA)
by Alex Vecchio 14 Sep '21

14 Sep '21

Dear Phenix Community, I would like to bring your attention to an NIH-funded Postdoc position in the Vecchio Lab <https://vecchio-lab.unl.edu> at the University of Nebraska studying membrane proteins and membrane protein assemblies using X-ray crystallography and cryoEM. We are looking for a recent or soon-to-be Ph.D., with experience in membrane proteins and one structural technique. Potential exists for the candidate to *acquire cryoEM expertise* during the postdoc training via a recently well-scored NSF fellowship. For more information, please read our ad HERE <https://jobrxiv.org/job/vecchio-lab-at-university-of-nebraska-27778-postdoc…> . To apply or for specific questions, please contact me at avecchio(a)unl.edu. All the best, Alex -------------------------------------------- Alex J. Vecchio, Ph.D. *Assistant Professor* University of Nebraska–Lincoln Department of Biochemistry Center for Integrated Biomolecular Communication 1901 Vine Street N113 / N114 Beadle Center [Lab / Office] Lincoln, NE 68588 avecchio(a)unl.edu 1 [402] 472-2933

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Assistant Researcher Senior Position in the KU Protein Structure Laboratory
by Lovell, Scott W 14 Sep '21

14 Sep '21

The Protein Structure and X-ray Crystallography Laboratory (PSXL) at the University of Kansas (KU) is seeking a full-time Assistant Researcher Senior to work on a variety of structural biology projects. As a core laboratory, the PSXL collaborates with multiple investigators to obtain structures of their proteins of interest using X-ray crystallography and delivers dozens of structures annually. Additionally, the PSXL is involved in NIAID funded R01 grants and manages the structural biology efforts for projects aimed at antiviral inhibitor development. As such, this position will involve structural biology work to facilitate the structure-guided development of inhibitors targeting the MERS-CoV and SARS-CoV-2 main proteases. For a full description of the position and to apply, GO TO: https://employment.ku.edu/staff/20030BR Regards, Scott __________________________________________________ Scott Lovell Ph.D., Director Protein Structure and X-Ray Crystallography Laboratory University of Kansas Del Shankel Structural Biology Center 2034 Becker Drive Lawrence, KS 66047 Office: SBC 1015 email: swlovell(a)ku.edu<mailto:[email protected]> phone: 785-864-3772 fax: 785-864-8141 https://psxl.ku.edu/ __________________________________________________

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Restricting real-space refinement and weights to specific atom selections
by Josh Cofsky 13 Sep '21

13 Sep '21

Hi all, I'm using phenix.real_space_refine to refine a model into a cryo-EM map. My local map resolution is highly variable across the molecule, and using a single map weight (the parameter shown in the Refinement Settings > "Other Options" in the GUI) on the whole model leads to poor map-to-model fit in some locations and overfitting in others. Potential solutions could be to: 1. assign different map weights to different segments of the model (based on a user-specified atom selection) OR 2. perform iterative refinements with different weight settings, holding different (user-specified) segments of the model fixed during each iteration (I suspect this isn't possible based on Pavel's message here: http://phenix-online.org/pipermail/phenixbb/2021-May/025037.html) Is either of these approaches (or another one that accomplishes the same goal) possible? I am using the Phenix GUI, but if this is only possible in command line, and you're willing to share an example command that accomplishes either of these tasks, please let me know. Thanks! -Josh (also, apologies if this is a duplicate message...still trying to figure out the phenixbb listserv)

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Extending a structure
by E Artikis 10 Sep '21

10 Sep '21

I have a pdb with a fibril composed of three identical chains. I'd like to expand the fibril from three to 15 chains. Is there a way to do this? It's essentially a copy/paste action, but I can't figure it out. Thanks!

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Phenix opens COOT but does not load map or model
by Boniecki, Michal 08 Sep '21

08 Sep '21

Hello, I used to be able (with previous phenix versions) load models into COOT after refinement. Now when I click open in COOT, only COOT window is open but neither maps or model are loaded.Also there is no "connected to phenix' displayed in COOT sidebar I have no problems with loading and displaying both in phenix or pymol (open with phenix or open with pymol buttons). Any suggestions how to solve it would be appreciated. COOT 0.9.5, phenix 1.19.2-4158 Michal

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Job posting: Scientist (crystallography) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 08 Sep '21

08 Sep '21

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology (crystallography). The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-protein and protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leido… Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research 8560 Progress Drive, C1012, Frederick, MD 21701 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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IUCr’s Committee on Data recent meeting minutes now online
by John R Helliwell 06 Sep '21

06 Sep '21

Dear Colleagues, I imagine that you will be interested in the IUCr’s Committee on Data recent meeting minutes which are now online here:- https://forums.iucr.org/viewtopic.php?f=39&t=441 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman IUCr Committee on Data

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copy R-free array from reference mtz using command line?
by Aaron Thompson 31 Aug '21

31 Aug '21

PhenixBB, I know this can be done via GUI, but is it possible to copy the R-free array from a reference mtz to a new mtz using the command line? I don’t see this as an option in phenix.reflection_file_converter. Thank you, Aaron

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NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 1 September
by Randy John Read 27 Aug '21

27 Aug '21

Hi, I’ve just learned that this online workshop is generally open, not just to members of the Norwegian Artificial Intelligence Consortium (NORA), and it’s free! Information, including the current programme and a link to registration, can be found here: https://www.nora.ai/events/AlphaFoldv2.0-and-RoseTTAFold-workshop%20.html I’ll be talking a bit about experiences with models from AlphaFold2 and RoseTTAFold, but the real draw should be talks by people who really understand these two deep learning algorithms: Minkyung Baek (first author on the RoseTTAFold paper, from David Baker’s group) and a representative of the DeepMind team that developed the two versions of AlphaFold. Sameer Velankar will also be there to talk about the exciting new AlphaFold database at the EBI. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Re: [phenixbb] NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 1 September
by Randy John Read 27 Aug '21

27 Aug '21

9 am CEST (Norway). Pretty early for our North American colleagues, especially those on the west coast! > On 27 Aug 2021, at 05:18, Robert Rose <rbrose2(a)ncsu.edu> wrote: > > Does the workshop start on August 31 at 9 am GMT? > > On Thu, Aug 26, 2021 at 2:27 PM Randy John Read <rjr27(a)cam.ac.uk> wrote: > Hi, > > I’ve just learned that this online workshop is generally open, not just to members of the Norwegian Artificial Intelligence Consortium (NORA), and it’s free! Information, including the current programme and a link to registration, can be found here: > > https://www.nora.ai/events/AlphaFoldv2.0-and-RoseTTAFold-workshop%20.html > > I’ll be talking a bit about experiences with models from AlphaFold2 and RoseTTAFold, but the real draw should be talks by people who really understand these two deep learning algorithms: Minkyung Baek (first author on the RoseTTAFold paper, from David Baker’s group) and a representative of the DeepMind team that developed the two versions of AlphaFold. Sameer Velankar will also be there to talk about the exciting new AlphaFold database at the EBI. > > Best wishes, > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building Fax: +44 1223 336827 > Hills Road E-mail: rjr27(a)cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Peptide bond to symmetry related molecule
by Damian Ekiert 24 Aug '21

24 Aug '21

Hi All, We are refining several structures in which the N-terminal residue of chain A appears to form a peptide bond to the C-terminal residue of its symmetry mate, chain A. In reality, the target protein consists of 4 identical helical repeats that pack end to end. Slippage and averaging over the 4 possible registers leads to the appearance of an infinitely long polymer in the crystal, with no breaks between protomers. Is it possible to enforce a peptide bond to symmetry mates in Phenix, and what is the easiest way to do this? I have found a several cases in the archives on how to deal with symmetry clashes, but struggling to figure out how to deal with a peptide bond. Thanks for your help! Best, Damian - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damian Ekiert Assistant Professor Skirball Institute | NYU School of Medicine Depts. Cell Biology and Microbiology damian.ekiert(a)ekiertlab.org www.bhabhaekiertlab.org

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Postdoctoral position in Computational Biochemistry
by Yasser Almeida 23 Aug '21

23 Aug '21

Dear all, The group of Computational Biochemistry of Prof. Elsa Sánchez-García at the University of Duisburg-Essen is announcing a Postdoc position focused on the computational design of chemical tools and inhibitors for the study of proteins and protein-protein interactions involved in cell state transition. The deadline for applications has been changed to September 30th. More information can be found at https://www.uni-due.de/computational-biochemistry. Best regards, Yasser -- Dr. Yasser Almeida-Hernandez Postdoctoral Researcher Computational Biochemistry group T01 R03 D45 Faculty of Biology University of Duisburg-Essen Universitätsstr. 2, 45117 Essen Email: yasser.almeida-hernandez(a)uni-due.de <%20yasser.almeida-hernandez(a)uni-due.de> Phone: +49 201 183 2457

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Project Scientist and Postdoctoral research positions in XFEL, ML, and material science computational methods
by Aaron Brewster 18 Aug '21

18 Aug '21

Hello, I'm excited to announce that two positions are immediately open in my group in the fields of material science, serial X-ray crystallography, and machine learning. Links to postings: Computational Project Scientist - https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=93507 Computational Postdoctoral Scholar - https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=93506 In these exciting roles, you will work in the Molecular Biophysics and Integrated Bioimaging Division on a project that will research adding advanced spatial and symmetry aware neural network training methods to small-molecule chemical crystallography and material science data processing. This will use AI methods developed as part of a close collaboration between teams at Lawrence Berkeley National Labs (LBNL), University of Connecticut, and MIT. The larger group is researching crystal engineering of hybrid coordination polymers towards achieving rational control over the optoelectronic properties of low-dimensional nanostructures. These positions are focused on the chemical crystallography aspect of the program, but the successful candidates will be expected to participate in all aspects of the program, including data collection at X-ray free electron lasers worldwide, data analysis on supercomputing facilities, structure solution, research on AI driven structure prediction, paper writing, and software management. Both roles are 3 year appointments. This work will be part of the Department of Energy Integrated Computational and Data Infrastructure for Science <https://insidehpc.com/2021/08/doe-funds-15m-for-integrated-computational-an…> Research program. Specific details follow. Berkeley Lab is committed to Inclusion, Diversity, Equity and Accountability (IDEA) <https://diversity.lbl.gov/ideaberkeleylab/> and strives to continue building community with these shared values and commitments. Berkeley Lab is an Equal Opportunity and Affirmative Action Employer. We heartily welcome applications from women, minorities, veterans, and all who would contribute to the Lab’s mission of leading scientific discovery, inclusion, and professionalism. In support of our diverse global community, all qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. *Computational Project Scientist* *What You Will Do:* - Design and train neural networks that allow determination of the unit cell and crystal orientations of small molecule crystals from sparse, randomly oriented diffraction patterns. This will involve curating training sets from simulated datasets and from existing and new experimental data that will be collected. - Research methods to scale training and use of these neural networks on multiple nodes in high performance computing environments. - Lead data collection and processing at X-ray free electron sources. - Maintain a detailed record of work performed. - Document and manage code developed using standard source control methods. - Publish in peer-reviewed journals. - Present research at seminars and conferences. - Assist Principal Investigator in developing grant proposals. - Document and maintain existing and new data processing software, including the cctbx build system. *What is Required:* - 2-5 years of relevant experience beyond the highest degree in Physics, Statistics, Crystallography, Artificial Intelligence, or a related field. - A strong background in Python, C++, or an equivalent platform for scientific computing. - A track record of critical thinking, problem solving, and mathematical intuition, demonstrated through publications and presentations. *Desired Qualifications:* - Familiarity with general Python scientific data packages such as NumPy, SciPy, and pandas. - Versed in modern coding practices for scientific computing, including algorithm design and evaluation, source code management under a revision control system like git, and incorporation of readable documentation and comments. - Expertise in computational approaches in at least one of the areas related to the research is required, including but not limited to small-molecular crystallography, structure solution and refinement, unit cell determination, neural network design, training, and evaluation, high speed computing, image analysis, large dataset analysis, graph theory, error propagation and statistics, signal processing, and GPU acceleration. - Familiarity with small-molecule material design and synthesis. - Strong analytical and organizational skills. - Excellent interpersonal, oral, and written communication skills. - Ability to work independently as well as part of a diverse team. *Computational **Postdoctoral Scholar* *What You Will Do:* - Design and train neural networks to model diffraction from small molecule crystals. This will involve curating training sets from simulated datasets and from existing and new experimental data that will be collected. - Assist in data collection and processing at X-ray free electron sources. - Maintain a detailed record of work performed. - Document and manage code developed using standard source control methods. - Publish in peer-reviewed journals. - Present research at seminars and conferences. * What is Required:* - PhD degree in Physics, Statistics, Crystallography, Artificial Intelligence, or a related field. - Experience in computational approaches in at least one of the areas related to the research, including but not limited to small-molecular crystallography, structure solution and refinement, unit cell determination, neural network design, training, and evaluation, high speed computing, image analysis, large dataset analysis, graph theory, error propagation and statistics, signal processing, and GPU acceleration. - Strong analytical and organizational skills. - Excellent interpersonal, oral, and written communication skills. - Ability to work independently as well as part of a diverse team. * Desired Qualifications:* - Familiarity with Python, C++, and general scientific data packages such as NumPy, SciPy, and pandas. - Familiarity with small-molecule material design and synthesis. Please do not hesitate to reach out to me for more information. Thank you, Aaron S. Brewster, PhD Computational Research Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

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Specifying import-time dependencies in _ext libraries?
by Russell M. Taylor II 18 Aug '21

18 Aug '21

I've developed an mmtbx_probe_ext module that makes use of objects defined in iotbx_pdb. I've added that library to LIBS= in the SConscript file, and it is able to link and run properly. However, when a Python script imports mmtbx_probe_ext, that load fails unless the same script has previously imported from iotbx: The following works: from iotbx.map_model_manager import map_model_manager import mmtbx_probe_ext as probe But the following fails: import mmtbx_probe_ext as probe from iotbx.map_model_manager import map_model_manager ImportError: /home/taylorr/rlab/cctbx-reduce-python27/build/lib/mmtbx_probe_ext.so: undefined symbol: _ZNK5iotbx3pdb9hierarchy5chain5atomsEi How do I tell Sconscript (or what do I do in my _bpl file) to tell Python that it needs to load the other module first? Thanks, Russ Taylor --- Russell M. Taylor II, Ph.D. russ(a)reliasolve.com taylor(a)redbudlabs.com rtaylor(a)aqueti.com russ(a)outloveracism.org www.cs.unc.edu/~taylorr

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Postdoc position in San Antonio, TX
by Yogesh Gupta 17 Aug '21

17 Aug '21

Dear Colleagues: My laboratory at the University of Texas Health Science Center at San Antonio is seeking an enthusiastic Postdoctoral Fellow to work on an NIH-funded project on SARS-CoV-2 and RNA modification. We will use X-ray crystallography, cryo-EM, and cell-based methods to address basic mechanistic questions and develop novel antivirals. These two papers describe our most recent work on SARS-CoV-2. Nature Communications. 2021 Jun 2; 12: 3287. PMID: 34078893. DOI: 10.1038/s41467-021-23594-y <https://www.nature.com/articles/s41467-021-23594-y> Nature Communications. 2020 Jul 24;11(1):3718. PMID: 32709886. DOI: 10.1038/s41467-020-17496-8 <https://www.nature.com/articles/s41467-020-17496-8> Preference will be given to applicants with demonstrated experience in purification and structural characterization of protein-nucleic acid complexes by X-ray crystallography with a strong interest in learning cryo-EM. An ideal candidate should hold (or soon expect to hold) a Ph.D. or equivalent degree in biochemistry/biophysics/structural biology and have no more than 3 years of postdoc experience. Salary is competitive and commensurate with experience. San Antonio is the nation’s seventh-largest city and is located at the edge of the beautiful Texas Hill County. San Antonio offers a rich, multi-cultural community, affordable cost of living, excellent weather, and a thriving biomedical industry. There is no state income tax in Texas. All Postdoctoral appointments are designated as security-sensitive positions. The University of Texas Health Science Center at San Antonio is an Equal Opportunity/Affirmative Action Employer, including protected veterans and persons with disabilities. If interested in applying, please send a short description of your research accomplishments and a CV with contact information of 3 references to Dr. Yogesh Gupta (email: guptay(a)uthscsa.edu). Yogesh -- Yogesh Gupta, PhD Assistant Professor of Biochemistry & Structural Biology Greehey Children's Cancer Research Institute University of Texas Health Science Center 8403 Floyd Curl Drive, San Antonio, TX, USA 78229 http://ccri.uthscsa.edu/YGupta.html

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Using AutoBuild to Complete a Model
by Whitley, Matthew J 17 Aug '21

17 Aug '21

Hello all, I have a very large protein with 16 copies in the asymmetric unit (nearly 15,000 total residues). Upon initial model building, ~30 residues at the N-terminus of each identical chain were not built. After building the reliable parts of the model and filling in other gaps and then refining that partial (but nearly complete) model, the N-terminal density has now improved to the degree that I can manually build a number of the missing residues in Coot. However, that means manually building the same series of residues over and over for each of the 16 identical chains. Is there a way to get AutoBuild to add these N-terminal residues for me to spare me the tedium of repetitive manual building? What I’ve gleaned from the documentation so far: >From the phenix.fit_loops documentation, it seems like that tool only works for filling in chain breaks, i.e. there is already modeled protein at each end of the missing region. That’s not the case for me because I’m trying to work backward toward the N-terminus. If I am reading the phenix.autobuild documention correctly, it sounds like there are two modes: (i) Standard mode - rebuild the whole protein from scratch, which does give the possibility of adding my N-terminal residues. However, I don’t want my nearly complete existing model to be rebuilt, I just want AutoBuild to try to add the missing N-terminal sequence to the existing model. (ii) Rebuild-in-place, which rebuilds the current model but doesn’t add or subtract any atoms. So that sounds like it’s not what I’m looking for because it won’t add the N-terminal sequence AND it rebuilds the existing model, which I want to keep exactly as is. Is there some series of options in AutoBuild that will allow me to just add missing residues (provided in the sequence file) but keep all the other currently existing residue in the input model exactly as they are? Happy to hear any advice you can give. Thanks, Matthew --- Matthew J. Whitley, Ph.D. Research Instructor Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine

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Post-doctoral fellow (M/F) in molecular and structural biology (Cryo-EM)
by Philippe Bénas 13 Aug '21

13 Aug '21

*/Posted on behalf of Dr. Franck Martin (CNRS IBMC, Strasbourg, France)/* */Please reply to F.Martin(a)ibmc-cnrs.unistra.fr/* */ /* */======================================================================================= /* */ /* */URGENT - Recovery Plan Project - Post-doctoral fellow (M/F) in molecular and structural biology (Cryo-EM)/* *Mission*** /You will be working as a post-doctoral researcher in a mixed public/private environment. The team 'Evolution of translation initiation systems in eukaryotes' of the unit 'Architecture and Reactivity of RNA' (UPR 9002 of the CNRS) of the Institute of Molecular and Cellular Biology (IBMC) of Strasbourg in association with the company Novalix. NovAliX is a 180+ employees society based in Illkirch (near Strasbourg). We offer to the pharmaceutical industry a complete range of services spanning biophysics, biochemistry, structural biology, chemistry & drug discovery. It is specified that this recruitment offer is part of the France Recovery Plan on a research collaboration project with a company which will be submitted to the DRARI for validation. The project will consist in structurally and functionally characterizing macromolecular complexes allowing the initiation of viral RNA of SARS-CoV-2. / *Activities* /The approaches used will be based on the use of cell-free translation extracts that will allow us to assemble and purify translation initiation complexes on our model messenger RNAs. The composition of these complexes will be determined by mass spectrometry and their structure by advanced structural approaches.The techniques used will be: / // /- Biochemical and molecular biology methods dedicated to the study of proteins and nucleic acids and in particular RNA/ /- Cryo-EM sample preparation, optimizing sample vitrification conditions./ /- Collect and analyse cryo-EM data. 3D reconstruction, structure determination and atomic model building./ /- Preparation of in vitro cell-free translation extracts/ // /The candidate will have to develop his/her project independently./ *Expected qualifications and proficiencies* /This includes the mastery of biochemical and molecular biology approaches for the purification of ribonucleoprotein complexes. Strong expertise in structural biology (Crystallography/Cryo-Electron Microscopy) especially on macromolecular complexes containing the ribosome will be considered as a plus. Ideally, the candidate should also be able to interpret electron density maps to establish atomic models of ribonucleic complexes containing the ribosome. The candidate must have defended his/her thesis in 2019 or 2020. / *Environment* /The candidate will join a biochemistry and molecular biology team specialising in translation initiation in eukaryotes. The structural part of the project will be implemented within the company Novalix. The Novalix cryo-EM platform is currently equipped with a Glacios microscope outfitted with a phase plate, Falcon 3 camera and microED setup. The candidate will spend 20% of his/her time in the public laboratory for the preparation of samples and 80% of his/her time at Novalix for the structural aspect./ More on IBMC: https://ibmc.cnrs.fr/en/ More on Strasbourg: https://www.visitstrasbourg.fr/en/welcome-in-strasbourg/ More on Alsace area: https://www.visit.alsace/en/ *Work constrains and professional risks* /The project will require the manipulation of radioactivity and the synthesis of RNA.Therefore, the mastery of good laboratory practices will be considered a plus./ *Application* /Applications will only be made via the recruitment website but feel free ton contact Dr. Franck Martin for any further details including application rules./ /Application website:/ /https://emploi.cnrs.fr/Offres/CDD/UPR9002-FRAMAR-006/Default.aspx?lang=EN/ *Salary* /Gross salary will be between 2675 and 3767 € per month according to working experience./ *Contact information*: /F.Martin(a)ibmc-cnrs.unistra.fr/

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experienced protein crystallographer needed
by Mooers, Blaine H.M. (HSC) 11 Aug '21

11 Aug '21

Dear all, Please share this job announcement with potential candidates. Associate Director of the Laboratory of Biomolecular Structure and Function The Laboratory of Biomolecular Structure and Function (LBSF) at the University of Oklahoma Health Sciences Center (OUHSC) seeks an experienced crystallographer to run the daily operations of the LBSF. The position is at the Assistant Professor of Research level. The candidate will be responsible for working with PIs to advance their structural biology projects. These efforts will include routine technical operations, developing new protocols to overcome challenging problems, and training the staff of user labs in protein purification, crystallization, data collection, and structure determination. The ideal candidate for this position will have a PhD and ten years of experience in macromolecular crystallography. The candidate will not be expected to write grant applications. Pluses in a candidate's background include experience with membrane protein purification and LCP crystallization, experience with Cyro-EM, or experience with other structural biology methods. The LBSF is part of a suite of core labs supported in part by the OUHSC Vice President of Research. The LBSF is also part of the Biomolecular Structure Core (BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural Biology (OCSB), which is based on the main campus in Norman. The BSC has contributed to the awarding of 23 million dollars in grant funding and 33 publications in the past nine years. The OCSB has been the focal point of Oklahoma's structural biology community for nine years. The community includes 50 labs at three major research institutions. The BSC will be a vital part of a new Center for Therapeutic Science. The center will coordinate and foster the drug development pipeline with the BSC playing a central role in structure-based drug design. Most of the 12 major users of the LBSF have cancer-related projects. One project led to the 2021 publication of crystal structures of RET Kinase bound to two drug molecules recently approved by the FDA for the treatment of non-small cell lung cancer. Most of the major users are members of the Stephenson Cancer Center, a National Cancer Institute-designated cancer center. The compensation level for this full-time position includes a generous benefits package. The position is based in Oklahoma City -- an affordable place to raise a family. To apply, please submit a cover letter, CV and contact information (name and email) for three references to Blaine Mooers, Director of the Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at ouhsc.edu. The position will remain open until filled. Application review will begin immediately. OUHSC is an equal opportunity employer and is committed to creating a diverse and inclusive environment for all employees. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Struc… COBRE in Structural Biology: https://www.ou.edu/structuralbiology

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Molprobity and D-amino acids
by Prasun Kumar 09 Aug '21

09 Aug '21

Hi All I am trying to solve a structure with D-amino acids. After refinement when I check the Molprobity results, I find a lot of C-beta outliers (a snapshot is appended below). I also get clashes between the carbonyl group of one residue and the side chain of the other. Any suggestion would be really helpful. C-beta outlier [cid:df63696e-1ce2-496d-9c9d-f4d35bd16015] Clashes [cid:9f665070-525b-497c-8009-e55ba533fdc1] Cheers PK

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