- phenixbb - phenix-online.org

molprobity in phenix 1.14
by Roberto Marabini 25 Feb '19

25 Feb '19

Hi, In the past (phenix 1.13) I have been able to execute molprobity with the command line: ============== phenix.python /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif map_file_name=/home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/molprobity.mrc d_min=2.200000 pickle=True pdb_interpretation.clash_guard.nonbonded_distance_threshold=None nproc=4 pdb_interpretation.clash_guard.nonbonded_distance_threshold=None ================== Unfortunately, for version 1.14 I get the error: ========================== Traceback (most recent call last): File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 310, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 193, in run map_params=params) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/molprobity/__init__.py", line 216, in __init__ molprobity_map_params=map_params.input.maps) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/experimental.py", line 198, in __init__ from mmtbx.command_line.map_model_cc import get_fsc ImportError: No module named map_model_cc ============== That is, there is an error in the line "from mmtbx.command_line.map_model_cc import get_fsc" By the way, if I just run the command: ============== phenix.python /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif ================== the program is executed without any problem. What should I do in order to execute molprobity.py with the option map_file_name. best wishes Roberto

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real space refine generates non-compliant PDB files
by Edwin Pozharski 22 Feb '19

22 Feb '19

Not sure whether anyone would care now that we got our marching orders to abandon PDB format and move to mmCIF, but the output of phenix.real_space_refine includes a number of lines that are not legit PDB records, i.e. this section ... REMARK 3 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.049 74053 ANGLE : 0.747 12.299 100513 CHIRALITY : 0.052 0.232 11312 PLANARITY : 0.006 0.069 13125 DIHEDRAL : 11.589 179.958 44947 MIN NONBONDED DISTANCE : 2.276 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.04 RAMACHANDRAN PLOT: OUTLIERS : 0.30 % ALLOWED : 8.63 % FAVORED : 91.06 % ROTAMER OUTLIERS : 8.76 % CBETA DEVIATIONS : 0 PEPTIDE PLANE: CIS-PROLINE : 3.7037037037 CIS-GENERAL : 0.0 TWISTED PROLINE : 1.85185185185 TWISTED GENERAL : 0.316455696203 REMARK 3 ... This does result in errors when this output PDB file is used as input to other software that is more stringent with format compliance. Cheers, Ed.

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Junior group leader opportunity in infection research (Braunschweig, Germany)
by Blankenfeldt, Wulf 22 Feb '19

22 Feb '19

Dear colleagues, I'd like to bring your attention to a job opening for a junior research group leader at the Helmholtz Centre for Infection Research in Braunschweig, Germany. The opening is broadly for infection research, and structural biologists should also feel encouraged to apply. The HZI has state-of-the-art facilities for x-ray crystallography and, through our participation in the CSSB on the DESY campus in Hamburg, to cryo-EM. We also have a protein sample production facility and equipment for biochemical/biophysical characterization. More details about the position and application requirements (deadline Feb. 28th!) can be found here: https://www.nature.com/naturecareers/job?id=672825 Best regards, Wulf ________________________________ Helmholtz-Zentrum f?r Infektionsforschung GmbH | Inhoffenstra?e 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig R?diger Eichel, Nieders?chsisches Ministerium f?r Wissenschaft und Kultur Gesch?ftsf?hrung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschr?nkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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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 13 Feb '19

13 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 07 Feb '19

07 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 03 Feb '19

03 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 31 Jan '19

31 Jan '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 30 Jan '19

30 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 29 Jan '19

29 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 28 Jan '19

28 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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This is a test
by Billy Poon 28 Jan '19

28 Jan '19

The Phenix website was down for a few hours, so this is a test to see if the bulletin board is working. -- Billy K. Poon 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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Announcement: SpringerBriefs in Crystallography
by Dorothee Liebschner 28 Jan '19

28 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

1 0

Announcement: SpringerBriefs in Crystallography
by Dorothee Liebschner 28 Jan '19

28 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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ISOLDE 1.0b2 release
by Tristan Croll 24 Jan '19

24 Jan '19

Dear structural biology community, I am very happy to announce that ISOLDE 1.0b2 is now available. All the details including documentation are available on the new ISOLDE website at https://isolde.cimr.cam.ac.uk, but the following is a short list of new features and improvements since ISOLDE 1.0b1: - added support for Windows. ISOLDE is now available for all three major operating systems. - many usability and stability improvements. In particular, ISOLDE is now much more helpful when your starting model is not yet quite simulation-ready. - No more need to delete unparameterised residues from your model. You can now choose to have ISOLDE simply ignore them for simulation purposes. - Real-time smoothing of the trajectory visualisation to reduce thermal jitter. - Direct handling of real-space maps (no need to convert them to structure factors first). - Live recalculation of structure factors and crystallographic maps from F/sigF data as model coordinates change. I do hope you find it useful. Best regards, Tristan

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(IUCr) Iron–sulfur clusters have no right angles
by Edward A. Berry 16 Jan '19

16 Jan '19

Iron–sulfur clusters have no right angles Nigel W. Moriarty and Paul D. Adams, Acta Cryst. (2019). D75, 16–20 <http://journals.iucr.org/d/issues/2019/01/00/rr5165/index.html> This agrees well with what we see in structures of respiratory complex II! But when I downloaded geostd.tar from https://sourceforge.net/projects/geostd/ and look in SF4.cif, I see: SF4 SF4 'Iron/sulfur cluster' Ion/Group/Compound 8 8 . 2009-09-01 2009-09-01 ~~~~ loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd SF4 FE3 S2 FE1 90.000 3.000 SF4 FE4 S2 FE1 90.000 3.000 SF4 FE2 S3 FE1 90.000 3.000 SF4 FE4 S3 FE1 90.000 3.000 SF4 FE2 S4 FE1 90.000 3.000 ~~~~ SF4 S3 FE2 S1 90.000 3.000 SF4 S4 FE2 S1 90.000 3.000 SF4 S2 FE3 S1 90.000 3.000 SF4 S4 FE3 S1 90.000 3.000 SF4 S2 FE4 S1 90.000 3.000 SF4 S3 FE4 S1 90.000 3.000 SF4 S3 FE1 S2 90.000 3.000 Did I get an outdated version?

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Postdoctoral position at UW-Madison
by Eric Montemayor 14 Jan '19

14 Jan '19

A postdoctoral position is immediately available in the laboratory of Professor Samuel Butcher at the University of Wisconsin-Madison. https://biochem.wisc.edu/faculty/butcher The Butcher laboratory is funded by the NIH to investigate the structure and function of RNA-protein complexes that regulate gene expression. Additionally, the lab is currently determining structure activity relationships for small molecules that regulate non-coding RNAs that play roles in neurodegenerative diseases. The Butcher laboratory is part of a vibrant research community at UW-Madison with state-of-the-art resources, such as the National Magnetic Resonance Facility at Madison (NMRFAM) and a newly established cryo-EM facility that will soon house a Titan Krios, Talos Arctica and Aquilos FIB/SEM electron microscope. The Butcher laboratory has established expertise in NMR, X-ray crystallography, SAXS, and myriad biophysical techniques. Additionally, we collaborate with local experts in cryo-electron microscopy. Thus, postdoctoral trainees in the Butcher lab are in a position to learn any aspect of contemporary structural biology. Recent publications: www.ncbi.nlm.nih.gov/pubmed/30215753 www.ncbi.nlm.nih.gov/pubmed/29717126 www.ncbi.nlm.nih.gov/pubmed/28887445 www.ncbi.nlm.nih.gov/pubmed/27194769 www.ncbi.nlm.nih.gov/pubmed/26655855 www.ncbi.nlm.nih.gov/pubmed/24837192 Requirements are a PhD in biochemistry or related scientific field. If interested, please send CV by email to: sebutcher(a)wisc.edu

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Refining an ion on a special position
by Shane Caldwell 12 Jan '19

12 Jan '19

Hi phenixbb, I've got a question related to refinement of an ion on a special position. I have a structure with an atom placed squarely on the C2 axis. I've been able to get a mostly-reasonable model by dropping in the ion at 0.5 occupancy and turning off repulsion for the ion in question, as Pavel describes here <http://www.phenix-online.org/pipermail/phenixbb/2018-February/023689.html>. It almost completely works. The thing I find now is that during refinement there can still be some random drift of the atom away from the symmetry axis, splitting from its symmetry ghost, while I know that it should stay perfectly coincident. My resolution is 3.1 and there's no indication of a multiple conformation, so a split isn't justified. The most parsimonious model should place the ion exactly on the C2. Is there any way to enforce that either 1. x, y = 0.0 in refinement, or 2. the ion is constrained to the xyz of the symmetric version of itself. Both should get to the same place, with the metal precisely on the axis, and precisely over top of it's symmetric counterpart. Thanks! Shane Caldwell Senior Fellow, Institute for Protein Design University of Washington Seattle, WA scald(a)uw.edu shane.caldwell17(a)gmail.com

3 5

atoms with unknown nonbonded energy type
by Danilo Belviso 11 Jan '19

11 Jan '19

Dear all, I am refining the structure of a cyclic peptide with having residues that are not in the ligand list of phenix. I would to perform unrestrained refinement by considering the very good resolution of the data. However, also in this case, phenix requires the restrain file of the ligand. I got cif file in two different way: 1) PRODRG server 2) by running phenix.elbow both produce the restrain file with no error message. However, by using such file in the refining, I get this error: Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 14 In the cif file, there are not atoms having 14 as energy type symbols. Could you suggest to what this message is referred to? How can I modify the cif to overcome the problem? Thanks in advance, Danilo -- Dr. Belviso Benny Danilo, PhD Istituto di Cristallografia (IC) Consiglio Nazionale delle Ricerche (CNR) via Amendola 122/o, 70126 Bari - Italy Tel ++39 080 5929273 Fax ++39 080 5929170 mail: danilo.belviso(a)ic.cnr.it web: users.ba.cnr.it/ic/crisdb00

2 1

Re: [phenixbb] Phenix installation on Debian9.6
by Billy Poon 09 Jan '19

09 Jan '19

Hi Danilo, I have a Debian 9.6 virtual machine running and Phenix is working after en_GB is installed. The problem is with the locale. It looks like en_GB is required even though another language is used. I had to install en_GB even if I'm using en_US. When I have only it_IT.UTF-8 installed, I get the en_GB error. After installing en_GB, the GUI works normally (see attached screenshot, phenix.png). To install en_GB with instructions from https://wiki.debian.org/Locale, 1) open a Terminal and become root 2) run "dpkg-reconfigure locales" 3) Select en_GB.UTF-8 (see attached screenshot, locale.png) 4) Select "OK" and complete process. You'll have to just choose your default language, but you should have it_IT.UTF-8 as your default 5) Verify that en_GB is available with "locale -a" (Mine is shown in a terminal in phenix.png) Changing the setting for Phenix 1) Go to the <phenix installation>/build directory 2) Type "export LC_ALL=it_IT.UTF-8" 3) Run the config_modules.sh script 4) Verify that "LC_ALL=it_IT.UTF-8" is in our programs. In phenix.png, I check that <phenix installation>/build/bin/phenix has LC_ALL set to it_IT.UTF-8 5) Phenix should run and the main GUI should pop up I suspect that because Phenix is not localized, we may be requiring an English language to be installed and maybe en_GB is a default. So in phenix.png, the dates for the projects are in Italian, but everything else is in English. Also, I think our number formatting is not localized, so decimal points will be "." instead of ",". I'm sending the images to you directly since the bulletin board has some size limit and the original message with attached images is waiting approval. -- Billy K. Poon 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 On Wed, Jan 9, 2019 at 8:53 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > Hi Danilo, > > I have a Debian 9.6 virtual machine running and Phenix is working after > en_GB is installed. The problem is with the locale. It looks like en_GB is > required even though another language is used. I had to install en_GB even > if I'm using en_US. When I have only it_IT.UTF-8 installed, I get the en_GB > error. After installing en_GB, the GUI works normally (see attached > screenshot, phenix.png). > > To install en_GB with instructions from https://wiki.debian.org/Locale, > 1) open a Terminal and become root > 2) run "dpkg-reconfigure locales" > 3) Select en_GB.UTF-8 (see attached screenshot, locale.png) > 4) Select "OK" and complete process. You'll have to just choose your > default language, but you should have it_IT.UTF-8 as your default > 5) Verify that en_GB is available with "locale -a" (Mine is shown in a > terminal in phenix.png) > > Changing the setting for Phenix > 1) Go to the <phenix installation>/build directory > 2) Type "export LC_ALL=it_IT.UTF-8" > 3) Run the config_modules.sh script > 4) Verify that "LC_ALL=it_IT.UTF-8" is in our programs. In phenix.png, I > check that <phenix installation>/build/bin/phenix has LC_ALL set to > it_IT.UTF-8 > 5) Phenix should run and the main GUI should pop up > > I suspect that because Phenix is not localized, we may be requiring an > English language to be installed and maybe en_GB is a default. So in > phenix.png, the dates for the projects are in Italian, but everything else > is in English. Also, I think our number formatting is not localized, so > decimal points will be "." instead of ",". > > -- > Billy K. Poon > 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 > > > On Wed, Jan 9, 2019 at 12:32 AM Tim Gruene <tim.gruene(a)psi.ch> wrote: > >> Dear Danilo, >> >> I agree that the language settings are probably not the cause of the >> problem. >> >> Maybe phenix created a segmentation fault. On recent versions of Debian, >> these >> show in the output of dmesg, but not necessarily in the terminal where >> you >> started phenix. >> >> Run phenix again, then type 'dmesg -T' to check if there is a >> segmentation >> fault. >> >> Best, >> Tim >> >> >> On Wednesday, January 9, 2019 9:15:39 AM CET Danilo Belviso wrote: >> > Dear Billy K. Poon, >> > >> > Thanks for your suggestion. My LANG variable is it_IT.UTF-8 and LC_ALL >> > in /build/bin/phenix is en_US.UTF-8. Unfortunately, once changed the >> > variable, reconfiguration as suggested doesn't fix up the problem. I >> > would like to say that the problem/warning related to "locale 'en_GB' >> > cannot be set" is just one of that shown in my first email. Likely, it >> > is also the less important. Indeed, I always had the same problem with >> > previous versions of phenix. The difference is that in that case phenix >> > worked and now it stops abruptly. It is just my opinion but the problem >> > could be in the list I posted in the first email. >> > >> > Thanks again for your suggestions. >> > >> > Regards, >> > >> > Danilo >> > >> > Il 2019-01-08 17:16 Billy Poon ha scritto: >> > > Hi Danilo, >> > > >> > > Another user on Debian 9 had a similar issue. What is the output to >> > > "locale -a" and what is your LANG and LC_ALL environment variables set >> > > to? And in the <phenix installation>/build/bin/phenix file, there is a >> > > place where LC_ALL is set. What is LC_ALL set to in that file? >> > > >> > > For unicode support, Phenix requires a language with UTF8 support >> > > (e.g. en_GB.UTF-8). During the installation, Phenix tries to determine >> > > the locale from the LC_ALL environment variable. By default, it gets >> > > set to en_US.UTF-8 if nothing can be found. However, on Debian 9, I >> > > got an error about en_GB even though en_US was available and set as >> > > the locale. >> > > >> > > On my Debian 9.6 virtual machine, I have en_US.UTF-8 and en_GB.UTF-8 >> > > installed and my phenix installation is using en_US.UTF-8. If you want >> > > to update the LC_ALL variable in the scripts in <phenix >> > > installation>/build/bin, >> > > >> > > 1) Set LC_ALL to the language you want with UTF-8 support (e.g. >> > > "export LC_ALL=en_US.UTF-8") >> > > 2) Run the "config_modules.sh" file in the <phenix installation>/build >> > > directory to change all the scripts to use the new locale. >> > > >> > > -- >> > > Billy K. Poon >> > > >> > > 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 >> > > >> > > On Tue, Jan 8, 2019 at 7:47 AM Danilo Belviso >> > > >> > > <danilo.belviso(a)ic.cnr.it> wrote: >> > >> Dear Rob, >> > >> >> > >> Thanks for your suggestions. I have just tried but it doesn't work, >> > >> unfortunately. >> > >> >> > >> Thanks again. >> > >> >> > >> Regards, >> > >> >> > >> Danilo >> > >> >> > >> Il 2019-01-08 15:43 Robert Oeffner ha scritto: >> > >>> Dear Danilo, >> > >>> >> > >>> >> > >>> I encountered the same problem with the locale when installing >> > >> >> > >> Phenix >> > >> >> > >>> on Ubuntu on Windows 10. The solution was to do from a bash shell: >> > >>> >> > >>> >> > >>> *cd /usr/share/locale* >> > >>> >> > >>> ** >> > >>> >> > >>> *sudo locale-gen "en_GB.UTF-8"* >> > >>> >> > >>> ** >> > >>> >> > >>> *sudo dpkg-reconfigure locales* >> > >>> >> > >>> I'm no linux expert so I wouldn't know if this procedure is >> > >> >> > >> general >> > >> >> > >>> enough that it would work on your system or if it would also solve >> > >> >> > >> the >> > >> >> > >>> other issues you mention before. >> > >>> >> > >>> Regards, >> > >>> >> > >>> Rob >> > >>> >> > >>> On 08/01/2019 14:32, Danilo Belviso wrote: >> > >>>> Dear all, >> > >>>> >> > >>>> I am intalling phenix on my Debian 9.6. >> > >>>> >> > >>>> My arch is adm64 thus I downloaded the phenix version named >> > >> >> > >> Kernel 2.6 >> > >> >> > >>>> (64-bit; CentOS 6). >> > >>>> >> > >>>> The installation procedure has been performed as suggested by the >> > >>>> >> > >>>> guide and no problems were obtained. However, by running phenix >> > >> >> > >> (after >> > >> >> > >>>> source phenix_env.sh) I get the follow output with several >> > >> >> > >> errors: >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >>>> >> > >>>> Error in sys.excepthook: >> > >>>> Traceback (most recent call last): >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", >> > > >> > >>>> line 886, in _excepthook >> > >>>> Error.show_exception_dialog(type, value, traceback) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Error.py" >> > > , >> > > >> > >>>> line 75, in show_exception_dialog >> > >>>> if (app.bug_timer.IsRunning() is False): >> > >>>> AttributeError: 'PhenixApp' object has no attribute 'bug_timer' >> > >>>> >> > >>>> Original exception was: >> > >>>> Traceback (most recent call last): >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/build/../modules/phenix/wxGUI2/ >> > > command_line/main.py",> >> > >>>> line 23, in <module> >> > >>>> run(sys.argv[1:]) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/build/../modules/phenix/wxGUI2/ >> > > command_line/main.py",> >> > >>>> line 17, in run >> > >>>> wxapp = App.PhenixApp(args) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", >> > > >> > >>>> line 70, in __init__ >> > >>>> wx.App.__init__(self, 0) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/site-package >> > > s/wx-3.0-gtk2/wx/_core.py",> >> > >>>> line 8628, in __init__ >> > >>>> self._BootstrapApp() >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/site-package >> > > s/wx-3.0-gtk2/wx/_core.py",> >> > >>>> line 8196, in _BootstrapApp >> > >>>> return _core_.PyApp__BootstrapApp(*args, **kwargs) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", >> > > >> > >>>> line 116, in OnInit >> > >>>> self.start_gui() >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", >> > > >> > >>>> line 144, in start_gui >> > >>>> callback_on_import=self.show_message) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking. >> > > py",> >> > >>>> line 280, in start_tracking >> > >>>> project_class="wxGUI2.Tracking.phenix_project_database", >> > >> >> > >> **kwds) >> > >> >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/ >> > > __init__.py",> >> > >>>> line 19, in start_tracking >> > >>>> callback_on_import=callback_on_import) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking. >> > > py",> >> > >>>> line 117, in __init__ >> > >>>> super(phenix_project_database, self).__init__(*args, **kwds) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/ >> > > project_db.py",> >> > >>>> line 39, in __init__ >> > >>>> self.choose_project(try_current_dir=True) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/ >> > > project_db.py",> >> > >>>> line 339, in choose_project >> > >>>> project_info = self.create_first_project() >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking. >> > > py",> >> > >>>> line 124, in create_first_project >> > >>>> from wxGUI2.Home import Projects >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Home/Proj >> > > ects.py",> >> > >>>> line 3, in <module> >> > >>>> from wxGUI2 import Base, Controls, PhilLayout, Windows, >> > >> >> > >> utils, >> > >> >> > >>>> Buttons >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/PhilLayou >> > > t.py",> >> > >>>> line 5, in <module> >> > >>>> from wxGUI2 import Base, Controls, Windows, utils, >> > >> >> > >> PhilInterface, >> > >> >> > >>>> FileDisplay >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/FileDispl >> > > ay.py",> >> > >>>> line 5, in <module> >> > >>>> import wxtbx.info_panels >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/inf >> > > o_panels.py",> >> > >>>> line 5, in <module> >> > >>>> import wxtbx.plots >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/plo >> > > ts/__init__.py",> >> > >>>> line 21, in <module> >> > >>>> locale.setlocale(locale.LC_ALL, '') >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/locale.py", >> > > >> > >>>> line 581, in setlocale >> > >>>> return _setlocale(category, locale) >> > >>>> locale.Error: unsupported locale setting >> > >>>> >> > >>>> >> > >>>> >> > >>>> Phenix starts by opening a window that states "locale 'en_GB' >> > >> >> > >> cannot >> > >> >> > >>>> be set" and abruptly closes so that I cannot use it. >> > >>>> >> > >>>> Do you have any suggestions to overcome such problems? >> > >>>> >> > >>>> I tried with Kernel 2.6 (64-bit; CentOS 5) and the 32-bit version >> > >> >> > >> too >> > >> >> > >>>> and the result is the same. >> > >>>> >> > >>>> Thanks in advance for your suggestions. >> > >>>> >> > >>>> Danilo >> > >>>> _______________________________________________ >> > >>>> phenixbb mailing list >> > >>>> phenixbb(a)phenix-online.org >> > >>>> http://phenix-online.org/mailman/listinfo/phenixbb >> > >>>> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > >> >> > >> _______________________________________________ >> > >> phenixbb mailing list >> > >> phenixbb(a)phenix-online.org >> > >> http://phenix-online.org/mailman/listinfo/phenixbb >> > >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > >> > _______________________________________________ >> > phenixbb mailing list >> > phenixbb(a)phenix-online.org >> > http://phenix-online.org/mailman/listinfo/phenixbb >> > Unsubscribe: phenixbb-leave(a)phenix-online.org >> >> -- >> -- >> Paul Scherrer Institut >> Tim Gruene >> - persoenlich - >> OSUA/204 >> Forschungsstrasse 111 >> CH-5232 Villigen PSI >> phone: +41 (0)56 310 5297 >> >> GPG Key ID = A46BEE1A >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > >

1 0

Phenix installation on Debian9.6
by Danilo Belviso 09 Jan '19

09 Jan '19

Dear all, I am intalling phenix on my Debian 9.6. My arch is adm64 thus I downloaded the phenix version named Kernel 2.6 (64-bit; CentOS 6). The installation procedure has been performed as suggested by the guide and no problems were obtained. However, by running phenix (after source phenix_env.sh) I get the follow output with several errors: (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion 'G_IS_OBJECT (object)' failed Error in sys.excepthook: Traceback (most recent call last): File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", line 886, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Error.py", line 75, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/home/bbdanilo/Programmi/phenix-1.14-3260/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module> run(sys.argv[1:]) File "/home/bbdanilo/Programmi/phenix-1.14-3260/build/../modules/phenix/wxGUI2/command_line/main.py", line 17, in run wxapp = App.PhenixApp(args) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", line 70, in __init__ wx.App.__init__(self, 0) File "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", line 116, in OnInit self.start_gui() File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", line 144, in start_gui callback_on_import=self.show_message) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking.py", line 280, in start_tracking project_class="wxGUI2.Tracking.phenix_project_database", **kwds) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/__init__.py", line 19, in start_tracking callback_on_import=callback_on_import) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking.py", line 117, in __init__ super(phenix_project_database, self).__init__(*args, **kwds) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/project_db.py", line 39, in __init__ self.choose_project(try_current_dir=True) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/project_db.py", line 339, in choose_project project_info = self.create_first_project() File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking.py", line 124, in create_first_project from wxGUI2.Home import Projects File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Home/Projects.py", line 3, in <module> from wxGUI2 import Base, Controls, PhilLayout, Windows, utils, Buttons File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/PhilLayout.py", line 5, in <module> from wxGUI2 import Base, Controls, Windows, utils, PhilInterface, FileDisplay File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/FileDisplay.py", line 5, in <module> import wxtbx.info_panels File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/info_panels.py", line 5, in <module> import wxtbx.plots File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/plots/__init__.py", line 21, in <module> locale.setlocale(locale.LC_ALL, '') File "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/locale.py", line 581, in setlocale return _setlocale(category, locale) locale.Error: unsupported locale setting Phenix starts by opening a window that states "locale 'en_GB' cannot be set" and abruptly closes so that I cannot use it. Do you have any suggestions to overcome such problems? I tried with Kernel 2.6 (64-bit; CentOS 5) and the 32-bit version too and the result is the same. Thanks in advance for your suggestions. Danilo

4 5

Jumping Rfree upon bulk solvent modeling
by Weinert Tobias (PSI) 08 Jan '19

08 Jan '19

Dear PHENIXBB community, i have come across a strange behavior in Phenix: * I copied Rfree-flags from a dataset with very slightly different unit cell * Refined the previously refined model against the new data * Rfactors in first round were good * Second round in refinement Rfree was up by 10 % just from the start during bulk solvent modeling and scaling * In another round Rfree was high in the beginning, and then dropped by those 10 % during bulk solvent modelling and scaling. * In yet another round Rfree started 10% lower than the previous round during bulk solvent modeling in the first cycle and then it jumps up again in the second cycle. What could be wrong? Many thanks and kind regards, Tobias Weinert

2 1

mmCIF in Phenix 1.14-3260
by Dominik Oberthuer 30 Dec '18

30 Dec '18

Dear all, I recently found that phenix.refine in version 1.14-3260 generates coordinate mmCIFs that the PDB deposition system can't handle. After struggling with this for some time I used an installation of Phenix 1.13-2998 I still have on my MacBook and used the mmCIF/PDB-conversion tool from this version and had no more trouble with uploading the mmCIF to the PDB. Maybe it is worthwhile to check which changes from 1.13 to 1.14 might have caused these issues. Thanks! Dominik -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberthuer(a)cfel.de

5 11