- phenixbb - phenix-online.org

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 08 Nov '21

08 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 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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 29 Sep '21

29 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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