- phenixbb - phenix-online.org

run phenix.refine in command line error
by 张士军 18 Feb '19

18 Feb '19

Dear I cannot run the *.params file when I use command line to run phenix.refine. Does have any default *.params file format, which I can edit it according to my case? Can you sent me one if does exist? Thanks . Best regards Shijun

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error installation dev-1.14.3405 - 1.14.3409
by Guenter Fritz 14 Feb '19

14 Feb '19

Dear phenix developers, I get errors trying to install latest builds from 1.14.3405, 3406, 3409 64bit centos6 on Scientific Linux machines still running 6.6 (kernel 2.6.32). 1.14.3395 installed without any problem. The downloaded file is OK. 1.14.3409 64bit centos6 installed on Ubuntu 18.04 without any problem. I also tried to install from source but got the same error output (see below). I googeled some error outputs - looks like some python error. Do I have to update finally? Best regards, Guenter Output trying to install from source: [guenter@msm68 phenix-installer-dev-3409-source]$ ./install --prefix=/home/software/PHENIX/1.14.3409/ --nproc=10 Traceback (most recent call last): File "./bin/install.py", line 20, in <module> from libtbx.auto_build import install_distribution File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_distribution.py", line 75, in <module> from libtbx.auto_build import install_base_packages File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module> from .package_defs import * File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/package_defs.py", line 18, in <module> from .bootstrap import Toolbox File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/bootstrap.py", line 14, in <module> import argparse ImportError: No module named argparse Similar from an installer: [guenter@msm68 phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6]$ ./install --prefix=/home/software/PHENIX/1.14.3405/ Traceback (most recent call last): File "./bin/install.py", line 20, in <module> from libtbx.auto_build import install_distribution File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 75, in <module> from libtbx.auto_build import install_base_packages File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module> from .package_defs import * File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/package_defs.py", line 18, in <module> from .bootstrap import Toolbox File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/bootstrap.py", line 14, in <module> import argparse ImportError: No module named argparse

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CryoEM post-doctoral position
by Hasan, Syed Saif 08 Feb '19

08 Feb '19

A post-doctoral research position is high-resolution single particle cryoEM is available immediately in my laboratory at the Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan) in Rockville MD. The post-doctoral researcher will have a choice of multiple projects in structural biology of membrane protein complexes involved in cancer and viral pathogenesis. The researcher will have independence to guide the direction of their research and to pursue novel ideas should they find an interesting scientific question related to the general focus of my laboratory. IBBR is home to a large community of structural biologists. Our new cryoEM facility houses a 200 keV Thermo Fisher Talos Arctica microscope equipped with a Gatan K3 direct electron detector. A 200keV Thermo Fisher Glacios microscope equipped with a Falcon III direct electron detector will be acquired soon. A 120 keV FEI Tecnai T12 TEM equipped with a CCD camera is available for negative stain imaging. In addition to the latest cryoEM facilities, IBBR offers access to tools in X-ray crystallography, NMR, small angle X-ray scattering, mass-spectrometry and computational biology, and provides opportunities to work closely in collaboration with scientists in industry and in national labs located nearby (i.e., NIH, NIST). Applicants should have experience in sample preparation, data collection and data processing for single particle cryoEM. Applicants who have received their PhD or MD/PhD degree should email me (sshasan(a)som.umaryland.edu) a single PDF file containing a short cover letter (no more than one page), a detailed curriculum vitae, contact information for three references, and up to 3 reprints of representative first authorship publication(s). The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology University of Maryland School of Medicine 108 N. Greene St., Baltimore, MD 21201 Institute for Bioscience and BiotechnologyResearch (IBBR) 9600 Gudelsky Drive, Rockville, MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan

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Real space vs reciprocal refinement
by Maheshwaran.V 04 Feb '19

04 Feb '19

Dear phenixbb! In the current version of phenix.refine contains the separate option for refinement: xyz (reciprocal space) and xyz (real space ). What does it mean and how it differs from the previous versions which had xyz and real space instead. So I just wanted to know what does it actually do? Can we run both of them simultaneously? Is it advisable to do both refinement for DNA ? - Mahesh India.

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Re: [phenixbb] Occupancy larger than 1
by Schnicker, Nicholas J 01 Feb '19

01 Feb '19

Hi Andrew, You should use group constrained refinement to link the occupancies of each isomer. You can see the documentation for how to implement it. https://www.phenix-online.org/documentation/reference/refinement.html#occup… Cheers, Nick From: <phenixbb-bounces(a)phenix-online.org> on behalf of Andrew Philip Thompson <andrew.thompson(a)adelaide.edu.au> Date: Wednesday, January 30, 2019 at 10:18 PM To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] Occupancy larger than 1 Hi Phenix BB, We discovered that a fragment had degraded in our crystallography condition and the product was observed bound in the resulting crystal structure. Unfortunately we have been unable to separate certain stereoisomers of this compound or its analogues, and so are looking to simultaneously model two of the isomers into the crystal structure. I have made a .cif file corresponding to each isomer and modelled them into my crystal structures with altloc tags A & B, however after refinement, the occupancy of the two adds up to more than 1 in some instances (ie. 0.51 and 0.53). I’ve never had this before when trying to model dual conformations of the stereoisomers. I tried to make the ligands the same residue number as discussed in a previous thread (http://www.phenix-online.org/pipermail/phenixbb/2011-March/016859.html), however neither coot or pymol will open the pdb file after refinement if I do this. Unfortunately I am unable to share the pdb file as we do not want to disclose the compound structure. Does anyone have any suggestions as to how to proceed? Thanks in advance, Andrew Andrew Thompson PhD Candidate Molecular and Cellular Biology School of Biological Sciences The University of Adelaide, Australia

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Occupancy larger than 1
by Andrew Philip Thompson 31 Jan '19

31 Jan '19

Hi Phenix BB, We discovered that a fragment had degraded in our crystallography condition and the product was observed bound in the resulting crystal structure. Unfortunately we have been unable to separate certain stereoisomers of this compound or its analogues, and so are looking to simultaneously model two of the isomers into the crystal structure. I have made a .cif file corresponding to each isomer and modelled them into my crystal structures with altloc tags A & B, however after refinement, the occupancy of the two adds up to more than 1 in some instances (ie. 0.51 and 0.53). I’ve never had this before when trying to model dual conformations of the stereoisomers. I tried to make the ligands the same residue number as discussed in a previous thread (http://www.phenix-online.org/pipermail/phenixbb/2011-March/016859.html), however neither coot or pymol will open the pdb file after refinement if I do this. Unfortunately I am unable to share the pdb file as we do not want to disclose the compound structure. Does anyone have any suggestions as to how to proceed? Thanks in advance, Andrew Andrew Thompson PhD Candidate Molecular and Cellular Biology School of Biological Sciences The University of Adelaide, Australia

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using phenix.refine results in coot on another computer
by Christian Biertuempfel 31 Jan '19

31 Jan '19

Dear all, I often run phenix.refine on a server but I would like to use the results on my laptop for further manual building. Is it possible to somehow export the todo lists (outliers/problems) identified in phenix.refine/molprobity as a script in order to use them in coot on another computer? Alternatively, is it possible to open the results from phenix.refine in a gui with coot integration on another computer (without access to the original data partition)? Cheers, christian ____________________________________________________________________ Dr. Christian Biertümpfel Max Planck Institute of Biochemistry Molecular Mechanisms of DNA Repair Am Klopferspitz 18 phone: +49 89 8578 3641 82152 Martinsried fax: +49 89 8578 3605 Germany ____________________________________________________________________

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IUCr Congress 2020 in Prague programme planning; data aspects
by John R Helliwell 30 Jan '19

30 Jan '19

Dear Colleagues, I draw your attention to the planning of IUCr Congress 2020 in Prague for which I am assisting with the programme planning on the data aspects:- http://forums.iucr.org/viewtopic.php?f=39&t=41 The Programme Committee is listed here:- http://www.iucr25.org/ipc/list.htm All best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

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unrestrained refinement
by Kaiser, Jens T. 29 Jan '19

29 Jan '19

Hi! I'm trying to do unrestrained refinement of a small molecule in phenix. I have done this many years ago, but it seems whatever I try, phenix.refine now complains about missing nonbonded energy type for all atoms. The pdb file I supply has the following format (just one line) HETATM 33 C81 UNK 1 3.117 14.425 18.765 1.00 1.45 C I tried unchecking all references to geometry restraints in the GUI, setting wc and wu to 0 I also started from a default .eff file and set all references to restraints to either True of False (depending what they said). I also tried the line from the phenix.refine documentation: phenix.refine ../cif_in/mkt_a.ent ../data/181119/proc/137C3/XDS_17000.HKL strategy=individual_sites wc=0 refinement.input.symmetry_safety_check=warning refinement.input.xray_data.r_free_flags.generate=True I'm using phenix v 1.14-3260 from an sbgrid environment. Any pointers welcome. Cheers, Jens

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Announcement: SpringerBriefs in Crystallography
by Dorothee Liebschner 29 Jan '19

29 Jan '19

Hi everyone, I would like to circulate the announcement of a new series of crystallography monographs entitled “SpringerBriefs in Crystallography” ( https://www.springer.com/series/16236). Areas of interest include structural biology. The announcement below is on behalf of the editor-in-chief, Prof. M. Nespolo. Best wishes, Dorothee Liebschner Series editor for biological crystallography, SpringerBriefs in Crystallography ========================================= Dear Colleagues, It is my pleasure to announce the launch of a new series of crystallography monographs under the title “SpringerBriefs in Crystallography”. They cover a new discipline within the “SpringerBriefs” collection, which publishes concise monographs with an intermediate scope ( https://www.springer.com/gp/authors-editors/book-authors-editors/springerbr… ). SpringerBriefs already covers 84 fields spanning a wide range from natural sciences to law, social sciences and more; crystallography is now the 85th field. The new series is published under the auspices of the International Union of Crystallography and all the manuscripts will be peer-reviewed by the series editors, as well as external reviewers when necessary. It takes an intermediate and so far uncovered place between articles published by the IUCr journals and full monographs. The IUCr publishes several types of articles in its journals (https://journals.iucr.org): • Research Papers, which are full-length manuscripts that normally do not exceed 15 journal pages (about 15 000 words); • Short Communications, for the presentation of topics of limited scope or for preliminary announcements of novel research findings; • Lead Articles, authoritative, comprehensive and forward-looking reviews of major areas of research interest (by invitation); • Feature Articles, focused surveys covering recent advances in an area of current research, which do not aim to be comprehensive, and are generally about ten journal pages (10 000 words); • Topical Reviews, which aim to capture the current trends of a field and are expected to be relatively short (about 6000 words and a maximum of 50 references, with half of those having been published in the last three years); • Letters to the Editor, which may deal with non-technical aspects of crystallography, its role, its propagation, the proper function of its Societies etc. • Scientific Commentaries, which discuss articles of particular importance for the readership of the journal. Full monographs spanning hundreds of pages are published in the IUCr/OUP monographs, and textbooks in the IUCr/OUP texts (https://www.iucr.org/publications/iucr-oup). SpringerBriefs in Crystallography aims at publishing shorter monographs, typically between 50 and 125 pages, where specific topics are dealt with more in detail with respect to what one could do in a Lead Article or Topical Review, in particular with a more pronounced accent on the background. Also, more space is given to some fundamentals which would not find place in a Lead Article or Topical Review, with the aim of providing the reader a more pedagogical introduction (whenever suitable) without the need to look for it in a separate text. Publications in this series help support the Outreach and Education Fund for the International Union of Crystallography (https://www.iucr.org/iucr/sponsorship/iucr-outreach-fund). The website of the new series is available at the address https://www.springer.com/series/16236, where you find more details as well as the responsible editor contact information, who upon request can provide you with a proposal form. On submission the responsible editor will then forward it to the series editors for discussion and approval. Please, feel free to forward this information to your colleagues who may be interested in publishing a monograph in this series. -- Project 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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