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phenix installation problem
by princeadam＠163.com 03 Dec '21

03 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 17 Nov '21

17 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 15 Nov '21

15 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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