- phenixbb - phenix-online.org

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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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 09 Nov '21

09 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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