- phenixbb - phenix-online.org

Online Course on Neutron Scattering Applications in Structural Biology (HANDS2021)
by Meilleur, Flora 27 Apr '21

27 Apr '21

ORNL Online Course on Neutron Scattering Applications in Structural Biology: https://conference.sns.gov/event/291/ Lectures: June 21 - June 25, 2021 Tutorials: June 28 - 30, 2021 2:00 pm - 5:30 pm EST Registration (free) is now open and will close May 14, 2021: https://conference.sns.gov/event/291/registrations/ This online course is designed for graduate students, post-doctoral researchers and faculty with knowledge of structure and function of biological macromolecules but with limited to no experience with neutron sciences. The course will cover the basics of deuterium labeling, small angle neutron scattering, neutron reflectometry, neutron spectroscopy, neutron imaging and neutron crystallography. Lectures will cover basic concepts, sample preparation, instrumentation and applications. Data collection and processing will be discussed in tutorials.

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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

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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>

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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/>

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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

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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 ]

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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

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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

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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 ]

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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

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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

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cif. file for AFITT
by Muhammad Bashir Khan 26 Mar '21

26 Mar '21

Hello all Could somebody explain how I can generate a cif. file of ligand for AFITT. I am using afitt in phenix refinement using the ligand cif. file generated by the elbow. But it complains. I have two different types of ligands in the structure. Thanks Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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Unusual ligand conformation
by Joel Tyndall 26 Mar '21

26 Mar '21

Hi all, We have been finalising a structure with a ligand complexed to heme. I have been checking the close to final structure and I noticed that the ligand looks distorted away from what one would expect. We use Phenix.refine We initially used the grade server for our restraints files. I also just used elbow to generate a new one. Looking at both, the restraints look reasonable (similar in both) however the initial output pdb from elbow is distorted further. The angles /lengths looked reasonable and are similar to small molecule structures (CCDC). The planarity of a bi-phenyl moiety is very distorted. [cid:[email protected]] Are we missing something? Do we need to tell phenix.refine to not over refine the model? Should elbow give a distorted model? Apologies if this is all online but my uni cant seem to access phenix.org! Thanks in advance Joel Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Skype: jtyndall Website | pharmacy.otago.ac.nz

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map to model FSC calculation
by C.J. 23 Mar '21

23 Mar '21

Hi All, I'm new to phenix and a bit confused to map to model FSC calculation. Which program should I use, phenix.mtriage or phenix.map_model_cc? If both work, what is the difference between them? Thank you! Jianhao

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Re: [phenixbb] FSC curves
by Pavel Afonine 19 Mar '21

19 Mar '21

Hi Juliana, > After running phenix real space refine with different refinement > strategies. My map-model FSC curve has some interesting features: > > 1. It does not starts at 1 as it does the map FSC curve, is that ok? > What could be causing this? > which one is it? Is it FSC(half_map1, half_map2) or FSC(experimental_map, model_map) ? > 1. It has a dip around 5-6Å, this deep can be a bit up or down > depending the refinement strategy I use, therefore the FSC model > at 0.5 can cut the resolution at 3.9 or 6 Å. What this deep mean? > Am I doing something wrong in the refinement? > How different these models are? > 1. The mask and unmask curves completely overlap, is that ok? > This suggests to me the map is probably already masked or somehow 'normalized'.. > 1. Also, my refinement shows a high clash score (15-20), if I change > the nonbonded_weight parameter from 100 (default) to higher values > the clash score decreases but the FSC curves gets lower them the > FSC curve crosses the 0.5 cutoff at 6A. > When it comes to clashscore, generally the lower the better but zero is not the goal. Looking at one of screenshots I see you have 2.42% of atoms with occupancy less than 1. Do you really see partially occupied atoms in 4A resolution map? Unlikely! So.. please check those out! I can run more diagnostics for you if you share maps and models (off-list of course!). Pavel

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on "Tutorial: Solving a structure with cryo-EM data using docking"
by Smith Lee 19 Mar '21

19 Mar '21

Dear All, For "Tutorial: Solving a structure with cryo-EM data using docking", it is easy to download the emd_20026_half_map_1_box.ccp4 and emd_20026_half_map_2_box.ccp4 from the emd-20026 depositation, but will you please let me know step by step how to get the tutorial used seq.dat, 20026_auto_sharpen_A.ccp4 (any other name for this file? Cannot find the exact name file in emd_20026 depositation), apoferritin_chainA_rsr.pdb (it mentioned "model refined against sharpened map", which sharpened map, and what was the refinement method ued?), run_denmod_dock.csh? I am looking forward to getting your reply. Best wishes, Smith

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Ligand refinment problum
by Muhammad Bashir Khan 18 Mar '21

18 Mar '21

Hello all; I have a crystal structure with four molecules per unit of the cell. It contains two different ligands. Four are similar while the fifth one is different. Placed all the five ligands manually by coot. Now I want to refine. Before refinement, I run the ReadySet to generate the cif. file. It shows an error. Then I supply the cif. file of both the ligand coming from the elbow, It still shows the following error. screenshot attached. Any help would be appreciated. Sincerely; Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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rotamers in real space refine
by Leonid Sazanov 17 Mar '21

17 Mar '21

Hi, We still have a problem of some Trp and Tyr residues going out of very clear density in high-resolution (~2.5 A) EM maps upon real space refine in phenix, even the latest version. Is there may be a more extensive rotamer library (including those pseudo-"outliers") available somewhere to be used in Phenix? Many thanks, Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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Migrating all phenix projects to a new location without breaking all of the file paths.
by Leonard,Paul G 15 Mar '21

15 Mar '21

Hi, Does anyone have instructions I can follow for how to move all of my phenix directories to a new location without messing up all of the file paths in each project. Our IT department wants to relocate files on our server which will change all of the top directory locations to something new so before that happens I think there is a way I can have a file that will allow me to recreate all of the phenix projects in the GUI with the new file paths but I can't recall how to do it. Thanks in advance for your assistance. Best wishes, Paul Institute Senior Research Scientist MD Anderson Cancer Center 1881 East Road Houston TX 77054 USA Tel: 732 397 8539 email: pleonard1(a)mdanderson.org 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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Is the Phenix website down?
by Joel Tyndall 14 Mar '21

14 Mar '21

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Re: [phenixbb] Question about Phenix refinement
by Dorothee Liebschner 12 Mar '21

12 Mar '21

Hi, This tutorial explains how to set parameters: https://www.youtube.com/watch?v=qB8W_6yuw5k&t=2s Best wishes, Dorothee On Fri, Mar 12, 2021 at 7:39 AM Zhang, Wen <wz15(a)iu.edu> wrote: > Hi, > > This is Wen from Indiana University. I have a question about the > refinement using Phenix. I got a Phenix Error, saying “Polymer crosses > special position element xxxxxxxxx. Use > allow_polymer_cross_special_position=True to keep going.” I also find this > keyword online, but am still not sure how I can change this key word. > Should I input the command somewhere? What should I do exactly? > > > > Thanks > > Wen > -- 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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Adding hydrogens back on lipids
by Noor Agip 12 Mar '21

12 Mar '21

Hi, Is there a way to add hydrogens back on lipids using Readyset? I tried this with no success. Best wishes, Noor

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Refining ligands in a structure
by Joel Tyndall 12 Mar '21

12 Mar '21

Hi folks, It has been a while since we have done much with phenix. We are refining a structure with a known ligand, voriconazole (exists on the pdb). We get an error regarding a lack of .cif file/restraints. Do we normally need to specify a cif file given this is a known ligand and can be retrieved in Coot? I assume that phenix would call on a known library of ligands/monomers that are known. Is this the correct library? phenix-installer-1.17.1-3660-intel-windows-x86_64\modules\chem_data\chemical_components\ Many thanks Joel Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Skype: jtyndall Website | pharmacy.otago.ac.nz

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Postdoctoral position in drug discovery at Vanderbilt University (Nashville, TN)
by Harp, Joel M 09 Mar '21

09 Mar '21

Postdoctoral position in drug discovery An opening is available in the drug discovery laboratory of Dr. Stephen Fesik for a post-doc in the field of protein x-ray crystallography. Responsibilities will include protein expression and purification, and all aspects of x-ray crystallography including preparation of protein-inhibitor complexes, crystallization, home/synchrotron data collection, and structure determination. Additional experiences in molecular biology including construct design, cloning, site-directed mutagenesis, and experience with recombinant protein expression in eukaryotic cells are highly preferred. The ideal candidate should be self-motivated and be able to communicate efficiently in a highly collaborative environment. Please send cv to jason.phan(a)Vanderbilt.Edu<mailto:[email protected]>

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Spatial query acceleration structure in cctbx?
by Russell M. Taylor II 08 Mar '21

08 Mar '21

As part of integrating the MolProbity tools more tightly with the CCTBX, I'm modifying the Probe code that will be shared by it and Reduce to use native CCTBX structures. One of the structures is a spatial map to accelerate the search for nearby atoms in a model. Before building my own (3D grid with near neighbors listed, ability to insert and remove atoms as they move), I wanted to check and see what was already available in the CCTBX. I looked at the page listing the CCTBX core objects and functions and did not see one, and searching for "spatial" and "accel" in the source tree did not turn up anything promising. Is there one already in there? If not, is this something that others would find to be a useful tool and, if so, where should it live? Otherwise, I'll make it part of Probe. 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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PAIREF Webinar (23rd March 2021, 15:00 CET)
by Petr Kolenko 08 Mar '21

08 Mar '21

Dear colleagues, We are pleased to announce the webinar on paired refinement to be held on March 23, 2021, from 3 PM (CET) to 4 PM (CET). This protocol provides an accurate estimation of the high-resolution cutoff (https://journals.iucr.org/m/issues/2020/04/00/mf5044/). The "PAIREF webinar" will be a free virtual event for up to 300 participants. The meeting will be recorded. Please register and receive your Zoom link here: https://kipl-indico.fjfi.cvut.cz/e/pairef We will cover: 1. Introduction to paired refinement. 2. Installation of PAIREF for CCP4 and/or PHENIX users. 3. Short tutorial (files will be provided). 4. Discussion. Feel free to contact us with your data. Best regards, Petr Kolenko, Martin Maly, Kay Diederichs and Jan Dohnalek

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error for "rosetta.run_tests"
by Smith Lee 06 Mar '21

06 Mar '21

Dear All, For rosetta installation for use in phenix, in the .bashrc I have: export PATH="/home/usrname/rosetta_src_2020.08.61146_bundle":$PATHexport PATH="/home/username/phenix11914122installdir/phenix-1.19.1-4122/build/bin":$PATH and I have the .bashrc file sourced. However when I run "rosetta.run_tests", I got the following error: --...... End of input processing Sorry: The RosettaScripts executable could not be located. Please set the environmental variable PHENIX_ROSETTA_PATH or add the appropriate directory to your PATH environment variable. ---- I am looking forward to getting your advice on how to solve the error issue. Smith

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phenix.molprobity geo
by Paul Emsley 04 Mar '21

04 Mar '21

Hello, I'd like to compare the restraints generated by Coot to the validation provided by molprobity. When I run phenix.molprobity on my model, it gives me (amongst other things) this: ----------------------- Histogram of nonbonded interaction distances: 1.87 - 2.42: 526 2.42 - 2.96: 3217 2.96 - 3.51: 3639 3.51 - 4.05: 5026 4.05 - 4.60: 6847 Nonbonded interactions: 19255 Sorted by model distance: nonbonded pdb=" O LEU A 21 " pdb=" H GLY A 26 " model vdw 1.874 1.850 nonbonded pdb=" H ILE A 71 " pdb=" O TYR A 80 " model vdw 1.920 1.850 nonbonded pdb=" H GLY A 34 " pdb=" O GLU A 54 " model vdw 1.925 1.850 nonbonded pdb=" O ILE A 71 " pdb=" H TYR A 80 " model vdw 1.937 1.850 nonbonded pdb=" HE ARG A 40 " pdb=" HG1 THR A 76 " model vdw sym.op. 1.955 2.100 -x+3/2,-y,z+1/2 ... (remaining 19250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. -------------------------- I don't understand this lilst. Should I be concerned by those interactions? Which of these atom pairs are contributing to the clashscore? Perhaps the details are in the .geo file? How do I get a .geo file? I googled, I didn't find the answer. How could I have found the answer without asking here? Thanks, Paul.

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Re: [phenixbb] executing Phenix in a python script on a Windows OS
by Muriel Gelin 02 Mar '21

02 Mar '21

Here is what I have: In a prompt: C:\Users\MG>C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat C:\Users\MG>phenix.refine Usage: phenix.refine [options] [reflection_file] [pdb_file] [parameter_file] -------------------------------------------------------------------------------- In python: source = subprocess.Popen(str(r"C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat"), stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) >>> phenix.refine Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'phenix' is not defined >>> py phenix.refine File "<stdin>", line 1 py phenix.refine ^ -------------------------------------------------------------------------------- If somebody see what is the problem. I'm afraid I am stuck ... Thank you all. Muriel Le 02/03/2021 à 11:03, gelin a écrit : > Dear Bernhard, > > Thank you for your answer. > > Executing phenix_env.bat in Windows command prompt works well, since I > can then execute phenix.refine in the prompt. > > So I tried to add in my python script something like that: > source = subprocess.Popen(my_path\phenix_env.bat, > stdin=subprocess.PIPE, stdout=subprocess.PIPE, > stderr=subprocess.PIPE) > Unfortunately, it doesn't work. I suppose the prompt environment is > not modified. > > Do you know how to do that in my python script so that I can then > execute something like: > xtriage = subprocess.Popen(["phenix.xtriage", my_mtz, > "parameters.reporting.log=" + "xtriage.log")], > stdin=subprocess.PIPE, > stdout=subprocess.PIPE, stderr=subprocess.PIPE) > > Thank you for you help. > > Muriel > > Le 2021-03-01 18:36, Bernhard Rupp a écrit : >> Here is what I did: >> >> Install phenix >> >> make a batch command in your path (eg phx.bat) that executes the >> environment setup, eg. >> C:\Phenix\phenix-installer-1.19-4092-intel-windows-x86_64\phenix_env.bat >> >> Open terminal, execute that batch (modify as you like), and there you go >> >> c:\data\Dropbox\Refinements\5okl>phenix.refine >> Usage: phenix.refine [options] [reflection_file] [pdb_file] >> [parameter_file] >> .... >> >> Best, BR >> >> -----Original Message----- >> From: phenixbb-bounces(a)phenix-online.org >> <phenixbb-bounces(a)phenix-online.org> On Behalf Of Muriel Gelin >> Sent: Monday, March 1, 2021 09:08 >> To: phenixbb(a)phenix-online.org >> Subject: [phenixbb] executing Phenix in a python script on a Windows OS >> >> Dear Phenix community, >> >> I wrote a python script to automate the processing of our data with >> Phenix. I'm not a developer by profession, but a crystallographer, and >> write scripts usually under Linux. My colleagues working under Windows >> asked me to share my script. >> >> I managed to run a simple python script under windows, no problem. But >> for a script that executes Phenix, it's not so easy (for me). >> >> Under Linux, I manage to source phenix_env.csh, but under Windows what >> is the command to setup Phenix in order to simply use phenix.refine >> or phenix.xtriage in my script? >> >> All I can find is this page >> https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/phenix/install-setup-run.html >> >> >> but I don't think it answers my question. >> >> Thank you in advance for your help! >> >> Muriel >> >> -- >> Dr Muriel Gelin >> >> Research Engineer >> Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced >> Biology, Chemistry, Informatics Studio" >> >> CNRS UMR 5048 - UM - INSERM U 1054 >> 29 rue de Navacelles >> 34090 MONTPELLIER Cedex - FRANCE >> http://www.cbs.cnrs.fr >> >> Tel: (33) 04 67 41 77 12 >> >> >> -- >> This message has been scanned for viruses and dangerous content by >> MailScanner, and is believed to be clean. >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > -- Dr Muriel Gelin Research Engineer Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced Biology, Chemistry, Informatics Studio" CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 12 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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on rosetta installation for phenix
by Smith Lee 02 Mar '21

02 Mar '21

Dear All, I have tried to install Rosetta for phenix use based on the guide in https://www.phenix-online.org/documentation/reference/rosetta_install.html. After the "tar xzf..." command, I added the directory for the installed rosetta (something like "export PHENIX_ROSETTA_PATH=/your-path-to-rosetta-here/") to my .bashrc (and in fact I also have added into /bash_profile) and sourced it. For the final step to build the interface for rosetta_refine, as for my gcc version is 8.3.1, I have deleted the original site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/, and exactly copied the content in https://www.phenix-online.org/documentation/extras/site.settings and save it as site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/. Command "nproc" displays 12, then I run "rosetta.build_phenix_interface nproc=12". In the running step for the above command, I remember it asked me "whether to install "sed" (I do not what is "sed" for), I answer "y" and "enter", it seems like the computer stopped. I opened another terminal, and all commands like "ls","cd" failed to work. I restarted the computer, but I cannot log into my centos username account anymore. I restarted the computer by initiating the centos secure start system, and deleted the export directory for the rosetta from the .bashrc and .bash_profile. In this way I restarted the computer and I can log into my centos user name account as usual. But as you know, my rosetta still did not work. Thus, will you please advice what is wrong for my installation fof the rosetta (for phenix use) and how to make it workable? I am looking forward to getting your reply. Best wishes, Smith

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Computational Crystallography Newsletter – Jan. 2021
by Nigel Moriarty 01 Mar '21

01 Mar '21

Folks The latest issue of the CCN is available on the website. Please consider contributing to future issues. 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 are available at www.phenix-online.org/newsletter. January 2021 <http://phenix-online.org/newsletter/CCN_2021_01.pdf> Articles - HKLviewer, a new 3D reflection data viewer for CCTBX <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=15> - Running CCTBX and PyMOL in the same Jupyter Notebook <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=26> Short Communications - PDB50: Celebrating 50 Years of the Protein Data Bank in 2021 <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=5> - Lessons from using the Cambridge Structure Database: II – Element specification X/Z <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=6> - The Importance of Being Positive: Charged ligands that bind nucleic acids <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=9> Fitting tips #20 - In-plane or out-of-plane H atom placement on the edges of aromatic rings <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=2> 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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executing Phenix in a python script on a Windows OS
by Muriel Gelin 01 Mar '21

01 Mar '21

Dear Phenix community, I wrote a python script to automate the processing of our data with Phenix. I'm not a developer by profession, but a crystallographer, and write scripts usually under Linux. My colleagues working under Windows asked me to share my script. I managed to run a simple python script under windows, no problem. But for a script that executes Phenix, it's not so easy (for me). Under Linux, I manage to source phenix_env.csh, but under Windows what is the command to setup Phenix in order to simply use phenix.refine or phenix.xtriage in my script? All I can find is this page https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/phenix/install-setup-run.html but I don't think it answers my question. Thank you in advance for your help! Muriel -- Dr Muriel Gelin Research Engineer Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced Biology, Chemistry, Informatics Studio" CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 12 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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on rosetta installation for phenix use
by Smith Lee 28 Feb '21

28 Feb '21

Dear All, I have tried to install Rosetta for phenix use based on the guide in https://www.phenix-online.org/documentation/reference/rosetta_install.html. After the "tar xzf..." command, I added the directory for the installed rosetta (something like "export PHENIX_ROSETTA_PATH=/your-path-to-rosetta-here/") to my .bashrc (and in fact I also have added into /bash_profile) and sourced it. For the final step to build the interface for rosetta_refine, as for my gcc version is 8.3.1, I have deleted the original site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/, and exactly copied the content in https://www.phenix-online.org/documentation/extras/site.settings and save it as site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/. Command "nproc" displays 12, then I run "rosetta.build_phenix_interface nproc=12". In the running step for the above command, I remember it asked me "whether to install "sed" (I do not what is "sed" for), I answer "y" and "enter", it seems like the computer stopped. I opened another terminal, and all commands like "ls","cd" failed to work. I restarted the computer, but I cannot log into my centos username account anymore. I restarted the computer by initiating the centos secure start system, and deleted the export directory for the rosetta from the .bashrc and .bash_profile. In this way I restarted the computer and I can log into my centos user name account as usual. But as you know, my rosetta still did not work. Thus, will you please advice what is wrong for my installation fof the rosetta (for phenix use) and how to make it workable? I am looking forward to getting your reply. Best wishes, Smith

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Collection of articles from ISDSB2019 now published in IUCr Journals
by John R Helliwell 26 Feb '21

26 Feb '21

Dear Colleagues, A collection of articles from the International Symposium on Diffraction Structural Biology 2019 held in Osaka is now online in IUCr Journals at https://journals.iucr.org/special_issues/2021/ISDSB2019 Several of these articles are open access. Best wishes, Atsushi Nakagawa, John Helliwell and Yuriko Yamagata

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NCS/pseudo-symmetry
by Muhammad Bashir Khan 25 Feb '21

25 Feb '21

Dear All; *I collected data set which can be easily processed in a space grouop P21 (P1211)* *at approx 3.7A. I procedeed with MR using phaser in phenix which give a solution with two copies. * ** There were 8 solutions ** Pdb and/or Mtz files have been written with results for 1 of these solutions ** Solution #1 written to PDB file: Khan_phaser.1.pdb ** Solution #1 written to MTZ file: Khan_phaser.1.mtz Solution #1 annotation (history): SOLU SET RFZ=3.4 TFZ=4.2 PAK=0 LLG=15 TFZ==5.5 RFZ=2.8 TFZ=27.6 PAK=5 LLG=1173 TFZ==36.5 LLG=1210 TFZ==36.8 PAK=6 LLG=1210 TFZ==36.8 SOLU SPAC P 1 2 1 SOLU 6DIM ENSE ense_1 EULER 7.6 86.4 3.3 FRAC 0.20 0.00 0.18 BFAC -1.90 #TFZ==5.5 SOLU 6DIM ENSE ense_1 EULER 7.6 86.4 3.2 FRAC 0.05 0.00 0.51 BFAC 1.60 #TFZ==36.8 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0444 #RMSD 1.29 #VRMS 1.64 Solution #2 annotation (history): SOLU SET RFZ=3.0 TFZ=5.5 PAK=0 LLG=10 RFZ=2.7 TFZ=25.6 PAK=0 LLG=1165 TFZ==34.8 LLG=1198 TFZ==34.0 PAK=4 LLG=1198 TFZ==34.0 SOLU SPAC P 1 2 1 SOLU 6DIM ENSE ense_1 EULER 10.7 83.5 177.9 FRAC 0.24 -0.00 0.14 BFAC -3.15 SOLU 6DIM ENSE ense_1 EULER 169.3 96.4 357.9 FRAC 0.91 -0.00 0.52 BFAC 1.82 #TFZ==34.0 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0705 #RMSD 1.29 #VRMS 1.65 Solution #3 annotation (history): SOLU SET RFZ=3.4 TFZ=4.1 PAK=1 LLG=-1 RFZ=2.8 TFZ=34.6 PAK=1 LLG=1146 TFZ==39.7 LLG=1185 TFZ==39.2 PAK=3 LLG=1186 TFZ==39.2 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 8.2 86.4 2.0 FRAC 0.01 -0.00 0.01 BFAC -1.69 SOLU 6DIM ENSE ense_1 EULER 8.3 86.4 2.0 FRAC -0.14 -0.00 0.34 BFAC 1.72 #TFZ==39.2 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0406 #RMSD 1.29 #VRMS 1.64 Solution #4 annotation (history): SOLU SET RFZ=3.5 TFZ=5.0 PAK=6 LLG=13 RFZ=2.9 TFZ=30.5 PAK=6 LLG=1156 TFZ==34.4 LLG=1183 TFZ==33.6 PAK=7 LLG=1183 TFZ==33.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.5 82.0 2.7 FRAC -0.18 -0.00 0.47 BFAC -2.89 SOLU 6DIM ENSE ense_1 EULER 359.5 82.1 2.8 FRAC -0.02 -0.00 0.14 BFAC 2.57 #TFZ==33.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0529 #RMSD 1.29 #VRMS 1.64 Solution #5 annotation (history): SOLU SET RFZ=3.5 TFZ=5.0 PAK=6 LLG=13 RFZ=3.0 TFZ=29.0 PAK=6 LLG=1115 TFZ==34.1 LLG=1178 TFZ==33.6 PAK=7 LLG=1178 TFZ==33.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.9 80.8 0.7 FRAC -0.18 -0.00 0.47 BFAC -1.57 SOLU 6DIM ENSE ense_1 EULER 180.1 99.2 180.7 FRAC 0.34 0.50 0.20 BFAC 2.47 #TFZ==33.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0405 #RMSD 1.29 #VRMS 1.64 Solution #6 annotation (history): SOLU SET RFZ=3.5 TFZ=4.6 PAK=1 LLG=-0 RFZ=2.8 TFZ=36.2 PAK=1 LLG=1136 TFZ==35.0 LLG=1169 TFZ==34.6 PAK=1 LLG=1169 TFZ==34.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.2 83.0 1.5 FRAC 0.06 0.01 0.03 BFAC -2.58 SOLU 6DIM ENSE ense_1 EULER 359.2 82.9 1.4 FRAC -0.09 0.01 0.36 BFAC 2.08 #TFZ==34.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0869 #RMSD 1.29 #VRMS 1.66 Solution #7 annotation (history): SOLU SET RFZ=3.5 TFZ=4.6 PAK=1 LLG=-0 RFZ=2.8 TFZ=35.3 PAK=1 LLG=1122 TFZ==35.4 LLG=1149 TFZ==34.5 PAK=1 LLG=1148 TFZ==34.5 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.2 82.5 2.4 FRAC 0.06 0.01 0.03 BFAC -1.93 SOLU 6DIM ENSE ense_1 EULER 180.8 97.5 182.4 FRAC 0.78 -0.49 0.31 BFAC 2.44 #TFZ==34.5 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0809 #RMSD 1.29 #VRMS 1.65 Solution #8 annotation (history): SOLU SET RFZ=3.4 TFZ=4.1 PAK=1 LLG=-1 RFZ=2.8 TFZ=33.9 PAK=1 LLG=1083 TFZ==38.5 LLG=1146 TFZ==38.5 PAK=4 LLG=1146 TFZ==38.5 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 8.1 86.1 2.6 FRAC 0.01 -0.00 0.00 BFAC -1.77 SOLU 6DIM ENSE ense_1 EULER 8.1 86.2 2.6 FRAC 0.17 -0.00 -0.33 BFAC 1.66 #TFZ==38.5 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0762 #RMSD 1.29 #VRMS 1.65 CPU Time: 0 days 6 hrs 35 mins 53.63 secs ( 23753.63 secs) Finished: Tue Feb 16 23:27:36 2021 *Got the following warnings:* WARNINGS -------- ------------------------------------------------------------------------------------------ Warning: Intensity moments suggest possibility of twinning. Tests based on possible twin laws will be more definitive. ------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------ Warning: The composition you have entered gives a solvent content of 87%, which is extremely unlikely. You should increase the composition. After running xtraige for the .mtz, I get this warning about NCS Frac. coord. : 0.157 -0.000 -0.333 Distance to origin : 119.294 Height relative to origin : 33.056 % p_value(height) : 8.504e-04. Translational pseudo-symmetry is very likely present in these data. Be aware that this will change the intensity statistics and may impact subsequent analyses, and in practice may lead to higher R-factors in refinement. Upon an attempt at initial refinement with different stratageis, the R-fators are stuck at Start R-work = 0.5066, R-free = 0.5233 Final R-work = 0.4831, R-free = 0.4965 The question is that there is something that is not being recognized for example merohedral twinning or that the NCS/pseudosymmetry is not being addressed correctly. Any suggestions would be highly appreciated. Regards; Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)
by Bjørn Panyella Pedersen 25 Feb '21

25 Feb '21

Dear colleagues, We have an open postdoc position. 3 days left before deadline. Come joint us. Great working environment, World-class science. Good work/life balance. /Bjørn ----------------------------------- Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. online posting: https://tinyurl.com/MBGpostdoc We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021.

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EMBO workshop on Molecular Neurobiology
by Janssen, B.J.C. (Bert) 24 Feb '21

24 Feb '21

Dear all, a gentle reminder of the upcomingEMBO workshop on "Molecular Neurobiology", a virtual meeting taking place on 21-25 May 2021. The deadline for registration, 28 February, is approaching fast. Only four days left. The virtual meeting brings together world leading scientists, group leaders and young researchers with a keen interest in the latest science occurring at the interfaces of structural biology, biophysics, molecular & cellular imaging and neuroscience. Given its cross-disciplinary nature, the meeting presents a broad overview of molecular neurobiology, ample opportunities for discussions and a sneak peek into the latest developments. See http://meetings.embo.org/event/20-molneuro for more information and application guidelines. Best wishes, Bert Bert Janssen Bijvoet Center for biomolecular research Utrecht University Padualaan 8, 3584 CH, Utrecht

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reminder - postdoc position at Astex
by Gabor Bunkoczi 23 Feb '21

23 Feb '21

Dear All, Just a quick reminder that Astex has an opening for a skilled post-doctoral researcher with an interest in software development. The aim of the project is to develop new methods for automated ligand fitting guided by experimental electron density/electrostatic potential maps, and will focus on locating, sharpening and classifying unmodelled regions of density, determining the identity of the binder using density shape and other physical properties derived from the surroundings, and subsequently fitting the molecule taking potential interactions with the environment into account. For more information about the position, please see the full advert: https://astx.com/wp-content/uploads/2021/01/SI-Post-Doc-2019-Mol-Sci-new-ad… Interested candidates should liaise with the HR department. For informal enquiries, please feel free to contact me directly. Best wishes, Gabor Bunkoczi Astex Therapeutics Ltd 436 Cambridge Science Park Cambridge CB4 0QA, UK This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.

1 0

Virtual Annual CCP4/APS Crystallographic School (2021) in the US
by Xu, Qingping 22 Feb '21

22 Feb '21

Dear Colleagues, We are pleased to announce the virtual annual CCP4/APS crystallographic school "From data collection to structure refinement and beyond" will be held on June 14-25, 2021 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2021/index.php. Dates: June 14 through 25, 2021 (with a weekend break on June 19 and 20th) Location: Virtual/Remote The school comprises two parts: remote data collection workshop and virtual crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA at APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections - lectures, tutorials, and hands-on (interactive troubleshooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 1st, 2021. To apply, visit https://www.ccp4.ac.uk/schools/APS-2021/application.php. Fees: There is no fee for attending the virtual school for the chosen applicants. We hope to see you at the school. Charles, Garib and Qingping

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Re: [phenixbb] Autosol help: FOM is great but map is trash
by Kay Diederichs 19 Feb '21

19 Feb '21

Hi Alex, I'm not a Phenix developer, but I have seen many cases like this, where reflections can be indexed with different cells, and one unit cell axis differs by a factor of 2. This just means that every second reflection (namely the odd one) along the reciprocal space direction corresponding to that axis is weak. It is not a priori clear which of the two choices is the best for structure solution and refinement. This depends on whether the weak reflections actually carry structural information (e.g. about tNCS with a translation close to 0.5), or whether they are a result of a crystal defect. It may sometimes happen that the crystal form is not suitable at all, since both choices don't refine well! Concerning P212121, P21212, P2122, etc: these are all primitive orthorhombic, and data processing alone cannot tell you which one is correct - they give identical data processing statistics. Typically, absent reflections along h00 0k0 00l should tell about screw axes, but in case of tNCS and two different cell choices the correct choice may not be obvious. Molecular replacement and subsequent refinement of all possibilities should help. Furthermore, contrary to what you write, it _is_ possible for all the orthorhombic space groups to account for reflections in both cell choices, so don't jump to conclusions too early. Just explicitly specify the (big or small) cell parameters in the data processing program of your choice! It may also help to try a different data processing package. Hope this helps, Kay Am 19.02.2021 um 04:28 schrieb phenixbb-request(a)phenix-online.org: > Message: 4 > Date: Thu, 18 Feb 2021 18:15:15 -0500 > From: Alex Johnson<algejohnson(a)gmail.com> > To:[email protected] > Subject: [phenixbb] Autosol help: FOM is great but map is trash > Message-ID:<6BE0A20E-F46B-482A-A675-22B685A2AFBE(a)gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Phenix team, > > I am attempting to phase a protein structure from SeMet-labeled crystals and have encountered some issues in using Autosol that appear unusual, as they have not been encountered by any members of my group. The short summary is that while I achieved great statistics from beam line collection and Autosol produces solutions with FOM (>0.4) from multiple crystals processed to ~2.4-3.0 A, the output maps are of poor quality and Autobuild can never build with Rfree <0.5. There is only one methionine for the ~30 kDa protein, but the crystals appear to have good anomalous signal with anomalous multiplicity >15 overall and delanon in the inner shell >0.5. There appears to be translational NCS and the dataset can be processed with good statistics in several space groups (P212121, P21212, P2122, etc) but this doesn?t solve the phase problem. The axis drops by half in processing in the P212121 versus P21212 space groups: from one crystal they are 48.37 101.56 110.39 90 90 90 (in P212121) and 101 > .62 48.35 55.19 90 90 90 (in P21212). > > If anyone in the community has encountered similar problems please let me know! I am all ears to any possible solutions and am also installing additional methionine for labeling but unsure whether this will overcome the other issues. > > Thanks, > > Alex Johnson > Postdoc, Kranzusch lab, Dana-Farber Cancer Institute > algejohnson(a)gmail.com <mailto:[email protected]> > > > > > >

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Scientist Antibody Production at the Institute for Protein Innovation in Boston, USA
by Christopher Bahl 19 Feb '21

19 Feb '21

Scientist Antibody Production Reports to the Head of Biological Discovery, Dr. Rob Meijers The Institute for Protein Innovation (IPI) is a nonprofit research organization advancing protein science to accelerate research and improve human health. Located on the Harvard Medical School campus in the Boston Longwood Medical Area, IPI is pioneering a new way of doing science that uniquely combines the freedom of academia with the high-throughput scaling of industry to take on transformative projects. IPI has built a robust platform and a repository of synthetic antibodies and other protein tools to share with the biomedical community through licensing and collaboration. The Institute’s deep protein expertise, collaborative spirit and fit-for-purpose antibodies are powering new biomedical and therapeutic discoveries for academic and industrial researchers worldwide. Job Overview IPI’s flagship project, the “Antibody Initiative,” aims to create well-characterized, synthetic antibodies against human cell surface receptors and their ligands, particularly those that are traditionally difficult to target. These antibodies may have high therapeutic and diagnostic potential but will also serve to enable basic biological discovery. The Scientist, Antibody Production will play an essential role in the high-throughput production, characterization and formulation of synthetic antibodies for this Initiative and other key IPI projects. Specifically, the successful candidate will join the Protein Group, a dynamic team generating high-quality antibodies and developing new technologies for conjugation. Having completed a doctorate in protein chemistry, the successful candidate will bring to the job experience in mammalian expression, purification and reagent-grade preparation of glycoproteins. The candidate will be adept in quality control and process management and reliably provide detailed documentation on experiments completed. The Scientist will work in close collaboration with the other Antibody Initiative team members and enjoy the opportunity to contribute to a wide array of novel biological discovery projects. As this position is highly collaborative, strong communication skills are needed. The Scientist will engage with outside collaborators, translate their biological questions into novel protein reagents and share these reagents with the larger research community through abstracts, presentations and publications. Responsibilities and Duties -Express, purify, and characterize glycoproteins from mammalian cells -Leverage robotics and automation to increase the quality and throughput of antibody production at IPI -Formulate and package antibodies for use by collaborators and customers -Supervise research associates and coordinate with other scientists to ensure efficient, high-quality antibody production -Actively lead the experimental design and data production for collaborations and scientific publications -Participate in meetings and conferences to engage and recruit outside research groups to participate in the Antibody Initiative Qualifications -PhD degree in mammalian protein expression, protein biochemistry, or structural biology -Well acquainted with best practices in cell culture and reagent production -Ability to work in a fast-paced, intellectually challenging environment -Enthusiastic team member with a strong commitment to mission and a desire to conduct impactful science -Good organizational and documentation skills -The ideal candidate will have recently completed a PhD and have a desire to explore a more entrepreneurial position IPI is an independent 501(3)(c) nonprofit research organization and an equal opportunity employer. The Institute celebrates diversity and is committed to creating an inclusive environment for all employees. If interested, please email your resume to . -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you.

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Autosol help: FOM is great but map is trash
by Alex Johnson 19 Feb '21

19 Feb '21

Hi Phenix team, I am attempting to phase a protein structure from SeMet-labeled crystals and have encountered some issues in using Autosol that appear unusual, as they have not been encountered by any members of my group. The short summary is that while I achieved great statistics from beam line collection and Autosol produces solutions with FOM (>0.4) from multiple crystals processed to ~2.4-3.0 A, the output maps are of poor quality and Autobuild can never build with Rfree <0.5. There is only one methionine for the ~30 kDa protein, but the crystals appear to have good anomalous signal with anomalous multiplicity >15 overall and delanon in the inner shell >0.5. There appears to be translational NCS and the dataset can be processed with good statistics in several space groups (P212121, P21212, P2122, etc) but this doesn’t solve the phase problem. The axis drops by half in processing in the P212121 versus P21212 space groups: from one crystal they are 48.37 101.56 110.39 90 90 90 (in P212121) and 101.62 48.35 55.19 90 90 90 (in P21212). If anyone in the community has encountered similar problems please let me know! I am all ears to any possible solutions and am also installing additional methionine for labeling but unsure whether this will overcome the other issues. Thanks, Alex Johnson Postdoc, Kranzusch lab, Dana-Farber Cancer Institute algejohnson(a)gmail.com <mailto:[email protected]>

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Post-Doctoral Position at the University of Illinois to Study Ribosome Structure
by Yury Polikanov 16 Feb '21

16 Feb '21

*Post-Doctoral Position in Structural Biology at the University of Illinois at Chicago (UIC) to Study the Structure and Function of the Ribosome* The Polikanov Laboratory at the University of Illinois at Chicago (IL, USA) is looking for a talented, skillful, and highly motivated researcher to fill the available *NIH-funded Post-Doctoral Scholar *position to study the structure and function of the bacterial ribosome. The research in the Polikanov Laboratory is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. More information about Dr. Polikanov research can be obtained from the most recent publications (*https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/50395623/public/?sort=date&direction=descending <https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/503…>*) or found on the web-page (https://bios.uic.edu/bios/people/faculty/yury- polikanov). The successful candidate will be involved in the determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography and potentially cryo-EM techniques. *Basic qualifications:* - PhD in chemistry, biochemistry , biophysics, or a related field; - Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); - Experience in structural biology (X-ray crystallography or cryo-EM); - Experience in the RNA biology field is not required but highly desired; *The successful candidate is also expected to:* - Act independently in terms of planning and executing the experiments; - Compile, analyze, and prepare data for publications; - Assist with training of graduate and undergraduate students. Review of applications will begin immediately and will continue until the position is filled. Interested candidates should apply by 04/16/2021 using the following link: https://jobs.uic.edu/job-board/job-details?jobID=142760 or email directly to Dr. Polikanov - yuryp(a)uic.edu. Please make sure to include CV, cover letter, and contact information for three references. *For full consideration, in **the cover letter, describe** how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group.* *The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans, and individuals with disabilities are encouraged to apply.* *Offers of employment by the University of Illinois may be subject to approval by the University’s Board of Trustees and are made contingent upon the candidate’s successful completion of any criminal background checks and other pre-employment assessments that may be required for the position being offered. Additional information regarding such pre-employment checks and assessments may be provided as applicable during the hiring process.* *The University of Illinois System requires candidates selected for hire to disclose any documented finding of sexual misconduct or sexual harassment and to authorize inquiries to current and former employers regarding findings of sexual misconduct or sexual harassment. For more information, visit **https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899 <https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899>*

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postdoctoral position in cryo-EM at LMB in Jan Löwe's group
by Jan Löwe 16 Feb '21

16 Feb '21

Dear all, My group has a grant-funded job opening for a postdoctoral structural biologist to work on problems in archaeal and bacterial cell biology. The aim is to understand cell division and vesicle formation at the molecular or even atomic scales. The work will involve state-of-the-art cryo-EM, biochemistry and tomography (and who knows, maybe even crystallography and/or NMR). We are surrounded here at LMB by many experts and a lot of exciting instrumentation, and given the current state of the project, only the sky (and our imagination) is the limit. Please find the job advert here: https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-… <https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-…> Please do get in touch if you would like to know more before applying. Best wishes, Jan Jan Löwe MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH UK email: jyl(a)mrc-lmb.cam.ac.uk website: http://www2.mrc-lmb.cam.ac.uk/groups/jyl

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Re: [phenixbb] rotamer outlier and clash socre
by Pavel Afonine 14 Feb '21

14 Feb '21

Hello Pan, """ I refined a cryo-EM data with 3.2 angstrom, the model fit well with the map, but the rotamer outlier is too high, about 8%. How can I decrease the value of rotamer outlier by realspace.refinement in Phenix GUI, and no need to adjust the residues one by one in Coot? """ if you used latest version of Phenix, which is dev-4146 as of today: http://phenix-online.org/download/nightly_builds.cgi?show_all=1 then this is not expected, because phenix.real_space_refine has built-in ability to detect which residues need a fix and does an exhaustive grid-search in chi-torsion angle space to optimize it against the map and local environment. If this happened using the latest version of Phenix, then this is an indication to me that something has gone wrong and we need to investigate. For this I'm asking to send all input files. Residues that phenix.real_space_refine was unable to fix for whatever reason are best to fit manually in Coot. And I can't agree more with Tristan -- all the great tools and automation are to help you not substitute you! So, checking manually is important! """ Another question is the value of clash score are also too high. """ You did not tell us the value, so no answer here! A general guidance: the lower the better, but zero is not the goal. """ When I set the nonbonded_weight to 10000 """ According to study we conducted recently: http://phenix-online.org/presentations/nb_weight.pdf this unlikely to be a great idea. Pavel

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rotamer outlier and clash socre
by xiaowp82＠hotmail.com 14 Feb '21

14 Feb '21

Hello everyone I refined a cryo-EM data with 3.2 angstrom, the model fit well with the map, but the rotamer outlier is too high, about 8%. How can I decrease the value of rotamer outlier by realspace.refinement in Phenix GUI, and no need to adjust the residues one by one in Coot? Another question is the value of clash score are also too high. When I set the nonbonded_weight to 10000, the clash score get better, but the value of rotamer outlier get worse. The high clash score maybe due to including hydrogens for refinement? Can I exclude hydrogen for refinement and how to do? Thanks ! Pan xiaowp82(a)hotmail.com

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Phenix ligand identification resolve was not able to finish on the first cycle
by Ahmad Khalifa 14 Feb '21

14 Feb '21

Hello, I want to use phenix.ligand_identification to identify a ligand. I used chimera's volume eraser to erase everything except for the ligand density. I then converted it to mtz. in the phenix.ligand_identification gui, I set reflection data type to difference map. When I ran the job, I got a lot of "Sorry, resolve was not able to finish on the first cycle". Regarding the mtz, I have to contour the map to 170rmsd to visualize it in coot, so something have to be wrong. I appreciate any input. Best regards.

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on phenix uninstall
by Smith Lee 13 Feb '21

13 Feb '21

Dear All, In order to install new version of phenix, should I uninstall the older version of phenix first? If needed, what are the command to uninstall the windows version of phenix and to uninstall the linux version of phenix? Smith

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The weblinks for the Daresbury Laue software source code and information
by John R Helliwell 12 Feb '21

12 Feb '21

Dear Colleagues, The weblinks for the Daresbury Laue software source code and information have become hidden from a simple google search. This short article at IUCr Journals makes clear where the software source code and information can now be found. See:- https://journals.iucr.org/s/issues/2021/02/00/me6120/index.html Best wishes, John Emeritus Professor John R Helliwell DSc

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unable to run coot
by Badmalia, Maulik 12 Feb '21

12 Feb '21

hello team phenix, I hope this email finds you well. I recently downloaded phenix for analysing our cryoEM data, before moving to the data analysis I decided to try the tutorial. I decided to use the autosharpen option first, I was able to access the tutorial but when I clicked on coot I repeatedly got a message saying that "Sorry: the 'coot' command could not be located. We have installed Coot to run on a CentOS platform and has the latest version of Coot on the system. I am a novice with linux and phenix. So any help in this regard would be highly appreciated. Do let me know if you have any questions. Regards, Maulik Maulik D. Badmalia Postdoctoral Researcher Laboratory of Medicinal Biophysics Alberta RNA Research and Training Institute Dept. of Chemistry & Biochemistry University of Lethbridge, Lethbridge, AB, Canada

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