- phenixbb - phenix-online.org

temp files
by James Holton 27 Apr '21

27 Apr '21

Hello all, Is there a way to configure phenix at install time (or perhaps post-install) to put temporary files under /tmp ? I just had to delete 20e6 temp files over NFS from a single user's phenix ligand identification run. The delete took almost a month. Apologies if I am neglecting to look somewhere obvious in the documentation, Happy Weekend! -James Holton MAD Scientist

4 7

Job posting: Scientist-I (Structural biology) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 21 Apr '21

21 Apr '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>

1 0

Caltech Postdoc Position
by Hoelz, Andre 19 Apr '21

19 Apr '21

The Hoelz laboratory at the California Institute of Technology seeks to recruit two outstanding postdoctoral scientists in structural cell biology. Our laboratory focuses on the structure-function relationships of the nuclear pore complex and associated nucleocytoplasmic transport machinery. This position requires a recent Ph.D. degree in biochemistry/biophysics with a strong background in biochemistry, x-ray crystallography, and/or cryo-electron microscopy/tomography. The successful applicant should be a highly motivated individual with good organizational, communication, and interpersonal skills, who is able to carry out a structure determination project from the development of recombinant protein expression systems to structure refinement. The laboratory is well-funded and equipped with modern biophysical instrumentation. Importantly, Caltech has an exceptional infrastructure for structural biology, including access to a high intensity, completely automated, state-of-the-art crystallography beamline at the Stanford Synchrotron Radiation Lightsource (SSRL), as well as an excellent cryo-electron microscopy facility with access to FEI Arctica and Titan Krios microscopes equipped with Gatan K3 cameras. The positions are available immediately and funded for 3+ years. Depending on performance, the position can be extended for additional years. To apply, please send your CV, a statement of research interests, and the names and contact information of at least two references to André Hoelz (hoelz(a)caltech.edu<mailto:[email protected]>). Selected Publications Lin, D. H., Hoelz, A.* (2019). The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725-783. Lin, D. H., Correia, A.C., Cai, S.W., Huber, F.M. Jette, C.A., Hoelz, A.* (2018). Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat. Commun., 2319. Huber, F., Hoelz, A.,* (2017). Molecular basis for protection of ribosomal protein L4 from cellular degradation, Nat. Commun. 8, 14354. Lin, D.,# Stuwe, T.,# Schilbach, S., Rundlet, E.J., Perriches, T., Mobbs, G., Fan, Y., Thierbach, K., Huber, F.M., Collins, L.N., Davenport, A.M., Jeon, Y.E., Hoelz, A.* (2016). Architecture of the symmetric core of the nuclear pore, Science 352, aaf1015. [Cover] Stuwe, T.,# Bley, C.J.,# Thierbach, K.,# Petrovic, S.,# Schilbach, S., Mayo, D.J., Perriches, T., Rundlet, E.J., Jeon, Y.J., Collins, L.N., Huber, F.M., Lin, D.H., Paduch, M., Koide, A., Lu, V., Fischer, J., Hurt, E., Koide, S., Kossiakoff, A., Hoelz, A.* (2015). Architecture of the fungal nuclear pore inner ring complex, Science 350, 56-64. Stuwe, T.,# Correia, A.,# Lin, D. H., Paduch, M., Lu, V. T., Kossiakoff, A. A., Hoelz, A.* (2015). Architecture of the nuclear pore complex coat. Science 347, 1148-1152. Hoelz, A.,* Debler, E.W., Blobel, G. (2011). Structure of the Nuclear Pore Complex, Annu. Rev. Biochem. 80, 613-643. --- André Hoelz, Ph.D. Faculty Scholar, Howard Hughes Medical Institute Investigator, Heritage Medical Research Institute Professor of Chemistry and Biochemistry Division of Chemistry and Chemical Engineering California Institute of Technology <x-apple-data-detectors://2><x-apple-data-detectors://2>1200 East California Boulevard<x-apple-data-detectors://2> Pasadena, CA 91125<x-apple-data-detectors://2> <x-apple-data-detectors://2><x-apple-data-detectors://2>U.S.A.<x-apple-data-detectors://2> Tel: 1-626-395-8480<tel:1-626-395-8480> (office) Tel: 1-626-395-3152<tel:1-626-395-3152> (lab) http://ahweb.caltech.edu<http://ahweb.caltech.edu/>

1 0

UnicodeEncodeError in Windows 10 Edu
by ‍김현우[ 학부졸업 / 생명과학부 ] 13 Apr '21

13 Apr '21

Hi everyone. I've installed open source pymol, coot, and phenix on my Windows 10 laptop. Pymol, python, and coot works fine, but when I launched phenix, it didn't work I tried both 1.18 and 1.19 version point-and-click installers. So I executed phenix on cmd, and the following error occured: ****************************************************************************** C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\build\bin>phenix Traceback (most recent call last): File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\build\..\modules\phenix\wxgui2\command_line\main.py", line 23, in <module> run(sys.argv[1:]) File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\build\..\modules\phenix\wxgui2\command_line\main.py", line 17, in run wxapp = App.PhenixApp(args) File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\modules\phenix\wxGUI2\App.py", line 70, in __init__ wx.App.__init__(self, 0) File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\conda_base\lib\site-packages\wx-3.0-msw\wx\_core.py", line 8628, in __init__ self._BootstrapApp() File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\conda_base\lib\site-packages\wx-3.0-msw\wx\_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\modules\phenix\wxGUI2\App.py", line 90, in OnInit self.setup_user_dir() File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\modules\phenix\wxGUI2\App.py", line 364, in setup_user_dir os.environ['PHENIX_DATA'] = wxGUI2.PHENIX_USER_DIR File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\conda_base\lib\os.py", line 422, in __setitem__ putenv(key, item) *UnicodeEncodeError: 'ascii' codec can't encode characters in position 9-11: ordinal not in range(128)* ****************************************************************************** I found out that unicode errors occur frequently and are easy to fix, but I can't figure out which file and which line I should manipulate. I'd appreciate any reply on this matter. Hyunwoo Kim

2 1

Please register - Phenix Workshop - April 14
by Paul Adams 08 Apr '21

08 Apr '21

Dear Colleagues, The Phenix developers will be holding another online *Phenix User Workshop on the 14th of April at 4-9pm PDT.* These times will work best for researchers in Asia and Australasia. The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. The workshop will cover aspects of macromolecular crystallography in Phenix, with the final emphasis based on the applicants’ research interests. To apply please fill out this form <https://forms.gle/X18KrWR6GvRUKYJ49>. We will make every effort to accommodate all applicants, but may need to defer some requests to a future workshop if demand is high. We are hoping this workshop will be a success, in which case we plan to host more in the future. *AGENDA:* *14 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Pavel Afonine - Real Space Refine - 5.15pm - Nigel Moriarty - Ligands and Restraints - 6.00pm - Jane Richardson - Validation - 7.00pm - Question/Answer session The recorded workshops are here <https://www.youtube.com/c/PhenixTutorials/playlists> for these and previous ones. Cheers, The Phenix Developer Team -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL ( http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL ( http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute ( http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source ( http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area ( http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley ( http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley ( http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ AshleyDawn(a)lbl.gov <LBenvenue(a)lbl.gov> ] [ 1-510-486-5455 ]

1 0

Automated water building into high-resolution cryo-EM maps (phenix.douse)
by Pavel Afonine 05 Apr '21

05 Apr '21

To all who reported multiple bugs and performance issues in phenix.douse: Phenix version dev-4196 and later now has all previously reported bugs and performance issues (slowness and memory consumption) fixed: http://phenix-online.org/download/nightly_builds.cgi?show_all=1 Please let us know should you find any more problems or have feature suggestions. phenix.douse is a tool to build water into high-resolution cryo-EM maps automatically. Background and details can be found here: http://phenix-online.org/presentations/water.pdf All the best! Pavel

1 0

Fwd: Thank you for registering - Phenix Workshops - April 7 & 14
by Nigel Moriarty 05 Apr '21

05 Apr '21

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 ---------- Forwarded message --------- From: Ashley Dawn <ashleydawn(a)lbl.gov> Date: Mon, Apr 5, 2021 at 9:56 AM Subject: Thank you for registering - Phenix Workshops - April 7 & 14 To: Ashley Dawn <ashleydawn(a)lbl.gov> Cc: Nigel Moriarty <nwmoriarty(a)lbl.gov>, Christopher Schlicksup < cjschlicksup(a)lbl.gov>, phenixdev <developers(a)phenix-online.org> Good morning, Thank you for registering for the Phenix Workshops that begin this Wednesday. *AGENDA: * *7 APR *(click to add to google calendar) <https://calendar.google.com/event?action=TEMPLATE&tmeid=MHRzaGc4ZDR0MDVpcjd…> - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Paul Adams - Phenix Overview - 4.30pm - Tom Terwilliger - Map Improvement - 5.45pm - Tom Terwilliger - Model Building - 7.00pm - Question/Answer session *14 APR * (click to add to google calendar) <https://calendar.google.com/event?action=TEMPLATE&tmeid=NXBhcmkxcTYzdmp1ZGN…> - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Pavel Afonine - Real Space Refine - 5.15pm - Nigel Moriarty - Ligands and Restraints - 6.00pm - Jane Richardson - Validation - 7.00pm - Question/Answer session Cheers, The Phenix Developer Team Ashley Dawn (she/her/hers) [image: A button for name playback in email signature] <https://www.name-coach.com/ashley-dawn> Senior Administrator Molecular Biophysics & Integrated Bioimaging Lawrence Berkeley Laboratory 1-510-486-5455

1 0

Please register - Phenix Workshops - April 7 & 14
by Paul Adams 05 Apr '21

05 Apr '21

Dear Colleagues, The Phenix developers will be holding an online *Phenix User Workshop on the 7th and 14th of April at 4-9pm PDT.* These times will work best for researchers in Asia and Australasia. The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. The workshop will cover aspects of macromolecular crystallography in Phenix, with the final emphasis based on the applicants’ research interests. To apply please fill out this form <https://forms.gle/X18KrWR6GvRUKYJ49>. We will make every effort to accommodate all applicants, but may need to defer some requests to a future workshop if demand is high. We are hoping this workshop will be a success, in which case we plan to host more in the future. *AGENDA:* *7 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Paul Adams - Phenix Overview - 4.30pm - Tom Terwilliger - Map Improvement - 5.45pm - Tom Terwilliger - Model Building - 7.00pm - Question/Answer session *14 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Pavel Afonine - Real Space Refine - 5.15pm - Nigel Moriarty - Ligands and Restraints - 6.00pm - Jane Richardson - Validation - 7.00pm - Question/Answer session Cheers, The Phenix Developer Team -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL ( http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL ( http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute ( http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source ( http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area ( http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley ( http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley ( http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ AshleyDawn(a)lbl.gov <LBenvenue(a)lbl.gov> ] [ 1-510-486-5455 ]

2 1

phenix.ligand_identification search_center
by Tanner, John J. 01 Apr '21

01 Apr '21

Phenix BB: I would like to use phenix.ligand_identification to analyze an electron density feature in the active site of an enzyme; however, I do not see how to specify search_center in the gui. Thus, the program places the ligands into a strong density feature on the surface of the protein. When I run it from the command line with search_center specified, it seems to ignore the search center coordinates and again places the ligands into the density feature on the surface. My command script: [tannerjj@europa ligandID]$ cat ligandID.com phenix.ligand_identification \ mtz_in = "/titan/tanner/MmP5CDH/THLP/MmALDH4A1_THLP8-1_003.mtz" \ mtz_type = diffmap \ input_labels = "FOFCWT PHFOFCWT" \ ligand_list = "DPR PRO HYP HZP UYA UY7" \ model = "/titan/tanner/MmP5CDH/THLP/MmALDH4A1_THLP8-1_003.pdb" \ ncpu = 4 \ output_dir = "/titan/tanner/MmP5CDH/THLP/ligandID/temp" \ number_of_ligands = 6 \ job_title = "THLP8-1_003 D,L-Pro and 4 OH-Pro stereoisomers" \ search_center = "-12.597 11.990 21.741" [tannerjj@europa ligandID]$ Thanks, Jack -- John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj(a)missouri.edu<mailto:[email protected]> https://cafnrfaculty.missouri.edu/tannerlab/ Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

2 1

phenix.local_aniso_sharpen
by Luca Pellegrini 31 Mar '21

31 Mar '21

Hi, Is there a way to estimate the resolution of the map obtained from phenix.local_aniso_sharpen? I find that it produces nice maps, but there’s no output information that I can see. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

2 1