- phenixbb - phenix-online.org

Rotamer restraints in phenix.real_space_refine
by Ashley Pike 01 Mar '19

01 Mar '19

Hi - Am I right in thinking that rotamer restraints behaves differently in latest official release (1.14-3260) compared to last but one official release (1.13-2998)? Issuing rotamer_restraints=True from command line or GUI used to give 0% rotamer outliers in the molprobity analysis at end of log in 1.13-2998 but now in 1.14 gives non-zero for same input model. It is as if they are not being applied. In the old log file it used to clearly print - **Update rotamer restraints*** after every macrocycle, in the 1.14 logs this is omitted. Many thanks, Ashley

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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?

2 3

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

1 0

Refining an ion on a special position
by Shane Caldwell 11 Jan '19

11 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

smaller the cell parameter of EM map
by dancingdream＠163.com 30 Dec '18

30 Dec '18

Dear all, The cell parameter of the EM map is always too large, which will make the model building program running very slow. But in factor, the structure is a smal part of cell. So can I smaller the cell parameter when I use phenix.map_to_structure_factors to convert the EM map to mtz file. Thank a lot! Wei

2 4

RapiData at SSRL 2019 - application closing data extended
by Smith, Clyde 26 Dec '18

26 Dec '18

Hi everyone, It has come to our attention that due to scheduled computer and power outages at SLAC over the Christmas/New Year period, the connection to the server supporting the RapiData 2019 page is down. Please use the following link to apply for the workshop: https://app.certain.com/profile/2831400 Because of this issue, we will be extending the closing date for applications to January 6 2019. If you have any problems don't hesitate to contact one of us. Cheers, Clyde Smith, Silvia Russi and Jeney Wierman (Organizers) csmith(a)slac.stanford.edu srussi(a)slac.stanford.edu jwierman(a)slac.stanford.edu

1 0

RapiData at SSRL 2019 reminder - just a week left to apply!
by Smith, Clyde 21 Dec '18

21 Dec '18

Hi all, A reminder that there is only a week left to apply for a place at the RapiData 2019 @ SSRL workshop. Applications close at the end of this month, December 31 2018. The workshop will be held from May 5-10 2019 on the SLAC campus in Menlo Park, California. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, Data collection strategies, X-ray light sources, X-ray detectors, Data reduction, Structure solution by MAD, SAD and Molecular Replacement, Complementary methods (spectroscopy and small angle scattering). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2019/ and use the links on the "registration" page to apply for the course. Successful applicants will be notified early in January 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in May 2019! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu jwierman(a)slac.stanford.edu csmith(a)slac.stanford.edu

1 0

Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 21 Dec '18

21 Dec '18

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 2019 issue is 20 January 2019. 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. 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

1 0

phenix.refine does not work with afitt
by Guenter Fritz 20 Dec '18

20 Dec '18

Dear phenix developers, I am trying to run phenix.refine with afitt (phenix 1.14 3260, afitt 2.4.1.2). However, I receive the an error: "Sorry: Unknown command line parameter definition: use_afitt = True" This I get on my mac or on my linux box . Is support for afitt discontinued? Any help is appreciated! Thanks and best regards, guenter

1 0

JRH Report on International Data Week 2018
by John R Helliwell 20 Dec '18

20 Dec '18

Dear Colleagues, I mention that my report on International Data Week 2018 can be found here:- http://forums.iucr.org/viewtopic.php?f=39&t=409 and which I imagine will be of general interest. All best wishes, John Emeritus Professor John R Helliwell DSc IUCr Representative to CODATA and Chairman of the IUCr Committee on Data

1 0

Postdoctoral position at the Drug Discovery Institute at Purdue University
by John M Hausman 17 Dec '18

17 Dec '18

Dear All: A position is available for a highly qualified and motivated postdoc with a strong background in Molecular/Cell Biology or Immunology. The successful applicant will be responsible for conducting research aimed at identifying and characterizing new drug targets for treatment of important human diseases. Activities may involve i) expressing and characterizing proteins that are upregulated in various disease states, ii) cloning, mutating, expressing and developing assays for studying functional aspects of the target proteins, iii) immunofluorescent staining of tissue sections from diseased tissues, iv) shRNA knockdown of desired proteins in cultured cells, and v) immunoblotting and other common biochemical assays. Management of day-to-day research goals and priorities, supervision of graduate students assigned to the same project, and mentoring of other research personnel regarding the design and execution of specific research methods/approaches may also be required. The lab is directed by Professor Philip S. Low in the new Drug Discovery Institute on the West Lafayette Campus of Purdue University. Other members of the lab are involved in designing new therapies for cancer, fibrotic diseases, infectious diseases, sickle cell disease, bone fractures and related pathologies, and autoimmune diseases, etc. Participation in some of these existing projects may also be required. Please send CV and list of three names of potential referees to: Philip S. Low Presidential Scholar for Drug Discovery Ralph C. Corley Distinguished Professor Department of Chemistry Purdue University 720 Clinic Dr. West Lafayette, IN 47907 Email: plow(a)purdue.edu<mailto:[email protected]> ________________________________

1 0

Help with AutoBuild
by Parthasarathy Sampathkumar 16 Dec '18

16 Dec '18

Dear All, These days my research often involves structure determination of the Antigen:Fab complexes, wherein the antigen structure is already known. Given this: (1). I would like to run AutoBuild in such a way that the program does not to touch antigen model, but only Re-builds only the Fab molecule; and (2). in some cases, due to structural-symmetry within the variable and constant domains of heavy- and light- chains, AutoBuild is searching and applying NCS operator while it is not present, and would like to avoid the same. How could these be done either in GUI or in command-line?!! Many Thanks in advance, Best Wishes Partha PS: Of course, when the data is at "high-enough resolution", I build Fab model manually after MR and Refinement. But, in the above case, resolution is only 3-ish angstrom.

2 1

speeding up effective resolution calculation
by Eric Williams 07 Dec '18

07 Dec '18

Greetings, all. I have what may be a naive question. :) I'm using phenix.resolution to calculate effective resolution, and I'm looking for ways to speed it up. I've tried a few different machine configurations, and it always takes around 20 minutes per structure. This is problematic for me, because I'm trying to collect data from the entire PDB. Does anyone here have experience using NumPy to optimize scripts and helpful suggestions for this case? Alternatively, how much speedup am I likely to get by rewriting the script in C and using it as a module? Thanks. :) Eric

3 2

New PDB archive reference paper now in NAR 2019 Database issue
by John Berrisford 05 Dec '18

05 Dec '18

An important <https://doi.org/10.1093/nar/gky949> new publication describing the activities and development of the Protein Data Bank (PDB), and authored by the whole wwPDB consortium, has been recently released in the 2019 Database issue of Nucleic Acids Research. Please see the following news release from the <https://www.wwpdb.org/news/news?year=2018#5c05780d3675962a10fcf7a9> wwPDB website: " <https://doi.org/10.1093/nar/gky949> Protein Data Bank: the single global archive for 3D macromolecular structure data has been published in the 2019 Database issue of Nucleic Acids Research. The paper was authored by "wwPDB Consortium" to underscore the importance of the global wwPDB partnership in managing the PDB archive. This article describes the development of the PDB under the stewardship of wwPDB, such as new archival content, master format and dictionary and major remediation efforts. The publication also emphasizes the importance of continued community interactions, the scientific and technical challenges the PDB faces, and charts the road ahead." -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/proteindatabank> http://www.facebook.com/proteindatabank <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

1 0

Re: [phenixbb] Molprobity values on output pdb
by Christopher Williams 30 Nov '18

30 Nov '18

Hi Boaz, Is it possible for you to send me (and just me, not the bulletin board) your file for testing? Thank you, if so. Alternatively, you can try using our alternate site at http:// altmolprobity .biochem.duke.edu, where a bugfix that probably addresses this issue is currently under testing. Thanks and good luck, -Christopher Williams ---Richardson Lab, Duke University On Fri, Nov 30, 2018 at 11:57 AM Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > Hi, > > > I noticed small differences between the molprobity > all-atoms clashscore reported in the output pdb file and the results > reported by the molprobity run (build 3318). > > > Cheers, > > > Boaz > > > > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of Life > Sciences Ben-Gurion University of the > Negev Beer-Sheva > 84105 > Israel > E-mail: > bshaanan(a)bgu.ac.il <bshaanan(a)bgu.ac.il> Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

1 0

Validation Completeness Issue
by Antoine Koehl 29 Nov '18

29 Nov '18

Hi, I’m in the process of uploading data to the PDB. While AIMLESS had estimated my completeness at 94% (similar to the XTriage value of 93.2%), the internal PDB validation through EDS estimates my completeness to be closer to 83.5%. This is a rather large difference. Both are using the exact same resolution range (49.57-4.00). Is there something that EDS does differently for estimating completeness? Please advise, Antoine

2 1

Test message
by Billy Poon 28 Nov '18

28 Nov '18

This is just a test. -- 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

1 0

Alternate conformer clash problem in phenix.refine
by Aaron Oakley 20 Nov '18

20 Nov '18

Salve! I am refining a protein/ligand complex where the ligand is bound with two conformers. Conformer A is covalently bound to a cysteine residue. Conformer B is free. I have prepared an appropriate cif dictionary for the ligand including info on handling the link. The problem is that during refinement, non-bonded interactions between the two conformers appear to not be switched off and their geometry becomes distorted. Is this diagnosis correct? If so, is there a way to manually switch off interactions? With thanks, a++ Aaron Oakley Associate Professor School of Chemistry and Molecular Bioscience | Molecular Horizons | Faculty of Science, Medicine and Health University of Wollongong NSW 2522 Australia T +61 2 4221 4347 | F +61 2 4221 4287 [cid:[email protected]]

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exclude clashes for non-symmetry contacts
by Edwin Pozharski 17 Nov '18

17 Nov '18

Is there some way to make phenix.refine to ignore clashes for specific pair(s) of chains? I am dealing with a rare case of twinning where same protein molecule exists in two orientations in the same unit cell. I tried just to duplicate the molecule and set initial occupancy to 0.5, but refinement fails (as I expected) saying that there are too many close contacts. Ideally, I would like to proceed with ignoring close contacts between, say, chains A/B. I am aware that one can exclude groups of residues from symmetry clashes, but these two copies are in the same cell. I guess I could try shifting one into the next unit cell and then excluding symmetry clashes, but even assuming that will work it is a rather ugly hack. The alternative is probably to define the second orientation as an alternative conformation. Aside from aesthetic objections, I don't want to lose the ability to restrain NCS - I need two orientations to be identical structures, and I am not sure yet whether I can use NCS groups defined via alternative conformers. Cheers, Ed.

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Normalized B-factor
by Mehmet Sen 16 Nov '18

16 Nov '18

Hello, I used the Structural Comparison tool to obtain normalized B- factor values for a couple of models, each with multiple chains. Is there an efficient way to visualize the normalized B-factor values (by writing over the old B-factor values) for the models, preferably in PyMOL? Thanks, Joyce V.

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Protonation of a symmetry-related His in Zn coordination sphere
by Priit Eek 16 Nov '18

16 Nov '18

Hi, I have a structure in which one of the His-residues of a Zn coordination sphere is from a symmetry-related protein chain. I specified the symmetry in an edits file so the coordination sphere is nice and plays well in refinement. I now added hydrogens to the model, but the His from the other chain does not get protonated correctly. I assume reduce doesn’t detect the presence of the symmetry-related Zn. It protonates NE, while that is the atom that interacts with Zn, but ND should be protonated instead. What would be the best way to fix this? And another question on the same matter: is it possible to specify a LINK in PDB between these atoms? Best regards, Priit ——— Priit Eek, PhD Researcher Department of Chemistry and Biotechnology Tallinn University of Technology Tel. +372 620 4387 priit.eek(a)taltech.ee

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Postdoc Position - Berkeley
by Paul Adams 14 Nov '18

14 Nov '18

Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 85784 Division: Molecular Biophysics & Integrated Bioimaging (Joint BioEnergy Institute) Date Opened: 11/1/2018 Summary: A postdoctoral position is immediately available to study the structure and function of macromolecular complexes and enzymes using biochemical, X-ray crystallographic and electron cryo-microscopy (cryo-EM) methods. The biological systems to be studied are: - Glycosyl transferases responsible for the synthesis of hemicelluloses in plants - Novel glycosyl hydrolases that are able to breakdown cellulosic material for biofuels production - Enzymes involved in lignin biosynthesis, degradation and valorization - Secondary metabolite and natural product enzymes This position will be part of the Structural Biology group of the Technology Division at the Joint BioEnergy Institute (JBEI) in Emeryville, California. To learn more about JBEI visit: http://www.jbei.org/ Duties: The successful candidate will have experience characterizing enzymes using biochemical techniques, and using crystallographic methods. Familiarity with cryo-EM methods would be helpful, but not essential. Robotic hardware for performing crystallization trials and imaging results are available. Crystals will be characterized and data collected using the beamline resources of the Berkeley Center for Structural Biology at the Advanced Light Source. For appropriate systems cryo-EM data will be obtained using in-house microscopes, the Bay Area Center for Cryo-EM, and other national user facilities. Qualifications: a Ph.D. in biochemistry, molecular biology, structural biology, chemistry or a related field. Demonstrated experience of scientific research using biochemistry techniques including enzymatic assays, and crystallographic methods. Experience with macromolecular crystallization techniques. Experience with cloning methods and protein purification methods would be helpful. Strong problem solving skills. Solid interpersonal skills and the ability to work in a team environment are critical. This is a full time, 2 years, postdoctoral appointment with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. You must have less than 3 years paid postdoctoral experience. Salary for Postdoctoral positions depends on years of experience post-degree. Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. To apply visit https://lbl.taleo.net/careersection/2/jobsearch.ftl?lang=en and search for the job number 85784 or visit: https://lbl.referrals.selectminds.com/jobs/crystallography-postdoctoral-sch… -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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R-free was improved, however, “Temp. fact. variance analysis” in “Validation” tool of COOT was worsened.
by Manami Torimoto 08 Nov '18

08 Nov '18

Dear all, By phenix.refine, I attempted to refine one molecule of protein. R-free was improved in certain wxc by setting the weight wxu manually, however, the results of “Temp. fact. variance analysis” in “Validation” tool of COOT was worsened. Why did such a thing happen? Thank you. Manami

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Low resolution refinement
by Ashu Sharma 06 Nov '18

06 Nov '18

Dear All, I am refining a ~7A single particle cryo-em structure of a protein. The protein has two domains and high-resolution crystal structures of individual domains are already known. I could fit these two crystal structures in the low resolution cryoem map of the full-length protein. I have two questions: 1) Is it acceptable to refine with side chains in this case? In most of the cases, with the guidane from crystal structures, side chains could be placed with reasonable confidence, particularly smaller ones. Should I restrict to poly-ala model or take the advantage of crystal structures and include side chains also? 2) When I tried to refine with side chains, longer side chains like K, R, Q, E which have weaker density tend to bend towards the backbone density. Is there a way to prevent this happening? Suggestions/comments from the community would be highly appreciated. Thanks ! Ashu

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Real-space correlation list for nucleotides?
by Boaz Shaanan 06 Nov '18

06 Nov '18

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(no subject)
by Matthew Bick 06 Nov '18

06 Nov '18

Dear Phenix BB administrator. Could you please post the following job opening to the mailing list? Thank you. Sincerely, Matthew Bick Senior Fellow Baker Laboratory for Computational Protein Design University of Washington The Institute for Protein Design, in the Department of Biochemistry at the University of Washington, currently has an outstanding opportunity for a full time X-ray Crystallographer Staff Scientist. The Institute for Protein Design is designing a new world of synthetic proteins for 21st-century challenges. PRIMARY RESPONSIBILITIES Collaborate with the Investigator and numerous researchers at the Institute for Protein Design on the X-ray crystal structure determination of de novo designed proteins. Manage the activities of research scientists and undergraduate research support with oversight of all protein-to-structure activities at the Institute for Protein Design. Design of new concepts, approaches and programs for structure determination of computationally designed proteins, of a diverse nature. Perform various specialized scientific investigative procedures in X-ray structure determination in collaborative support of numerous research projects with minimal input from Investigator. Use bio-informatics tools and pertinent laboratory and public databases, including the Protein Data Bank (PDB), and information resources to support gene-to-structure research, including deposition of atomic coordinates in the PDB for archival, sharing, and publication. Direct the activities of technical support staff in the Baker lab and at the Institute for Protein Design in collaboration with other research staff. Collaborate with other research staff, postdoctoral fellows and graduate students to select and maintain relevant protein research equipment to insure the lab meets required current and future needs. Direct the development of new protein crystallization and X-ray structure determination strategies, and ascertain if they effectively addresses needs. Manage complex multi-task projects directed at the design, production and structural characterization of numerous de novo designed proteins with higher order function. Train laboratory research staff, postdoctoral fellows and graduate students in protein X-ray crystallography, as well as wet lab equipment for protein production, structural elucidation, and biochemical characterization. Direct projects with undefined time lines and uncertain outcomes requiring analysis from multiple perspectives. Use expert knowledge and judgment to develop new methods and techniques for obtaining solutions. MINIMUM QUALIFICATIONS: Ph.D in Biochemistry, or related field, and X-ray Crystallography +5 or more years of related experience Technical proficiency, scientific creativity, collaborative ability, as well as independent thought. Advanced expertise in X-ray crystal structure determination, both computational and wet lab areas, with a full understanding of the underlying principles and concepts. May be recognized as a leader in their area of expertise. Recognized as a resource for others to use in dealing with complex protein structure determination, computational and wet lab methods, equipment, processes, or procedures. Anticipate future needs in technology support. In-depth understanding of organizational structure both within and outside the work unit, including the role of each position in the group and in other groups. Ability to develop innovative processes to achieve goals. Direct others to develop essential tasks. Review work activities to determine where new information could improve processes or move projects forward. DESIRED QUALIFICATIONS: Ph.D. degree in an appropriate field of science or technology or equivalent in education and experience AND total of six year’s research experience in protein biophysics, X-ray crystallography, computational biology and bioinformatics specifically in the X-ray crystal structure determination. Interested candidates should send a cover letter and CV to Matthew Bick at bickm(a)uw.edu.

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Speeding direct summation ?
by Clement Degut 02 Nov '18

02 Nov '18

Hi, I have (very) high resolution data, for which direct summation method seems to give significantly better map than FFT (i.e. visible hydrogen vs not). My main problem is that refinement got from quite slow, to barely not really possible to handle slow. I have 2 question from that : Am I looking at an artifact ? Meaning should at this resolution (0.84A for CC1/2 at 30% and good overall statistics) see extreme difference between map quality with direct summation vs FFT ? And if yes, can I speed the process compiling phenix with openMP on our cluster ? Or shoul I just become patient ? Many thanks Clément

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Postdoctoral position in Indiana University School of Medicine
by Takagi, Yuichiro 02 Nov '18

02 Nov '18

Postdoctoral Fellow, Takagi Laboratory (https://medicine.iu.edu/research/faculty-labs/takagi/), Department of Biochemistry and Molecular Biology Indiana University School of Medicine We are looking for a highly motivated postdoctoral follow with a background in structural biology (X-ray crystallography, cryo-EM), to work on NIH-funded projects studying multi-protein complexes involved in eukaryotic transcription regulation. Who We Are: My laboratory is interested in understanding the mechanisms of assembly, structure and function of large multi-protein complexes -“molecular machines” - involved in eukaryotic gene regulation, utilizing both cryo-EM and X-ray crystallography. We are particularly interested in the Mediator complex in both yeast and humans. We believe that development and implementation of novel technologies is the key to unlocking the mysteries of how highly complex molecular machines (e.g. Mediator) function. Therefore, our overall research objective is two-fold: (i) development of novel technologies for studying multi-protein complexes, and (ii) application of these technologies to elucidate the structure and function of the Mediator complex. In addition, we have developed a novel technology for producing pure preparations of difficult-to-express proteins and protein complexes, which has enabled several exciting ongoing projects with outstanding collaborators, including work on: plant RNA polymerases, DNA helicases, DNA repair complexes, RNA editing complex, and insulator complex. What We Offer: State-of-the art protein and protein complex expression technologies (patent pending) enabling expression of difficult-to-express, problematic proteins and protein complexes Accessibility to crystallization drop-setting robots, home X-ray sources, Synchrotron data collection at the Advanced Photon Source (APS) at Argonne National Laboratory (within a 3 hour drive from our lab), as well as electron-microscopy (EM) facility: Titan Krios, Talos Artica, and JOEL-FS3200 A one-on-one mentoring opportunity by which a postdoctoral fellow can learn the craft of designing research strategy, preparing compelling grant proposals, and paper-writing and presentation skills The opportunity to work with multiple outstanding collaborators Who Should Apply: This position could be a great fit for you if: you have the expertise and experience in X-ray crystallography, and want to apply such skills toward structure determination of highly complex multi-protein complexes you are interested in learning and developing for the cutting-edge protein complex engineering and expression technologies you would like to extend your skill sets to cryo-EM you are self-confident and can communicate with the PI, other lab members, and collaborators with ease, and enjoy discussing research results and how to overcome technical challenges the specific research focus of our laboratory inspires you you love to gather information from the literatures and helps generate creative ideas and technical solutions you relish working on technically challenging problems, which often require an extended persistent effort to crack Job Description, Qualification, and Expectations: Primary activities in this position include, but are not limited to: Expression and purification of the protein complexes for biochemical and structural studies (cyo-EM, crystallization Structure determination of the protein complexes by cryo-EM or/and X-ray crystallography Biochemical assays to characterize the recombinant protein complexes Providing intellectual contributions to the projects including writing manuscripts, fellowship application and helping PI for grant applications Ph.D. in structural biology (X-ray crystallography, cryo-EM) is strongly preferred. If interested, please email a cover letter, CV, and two reference letters to ytakagi(a)iu.edu Applications will be screened until a suitable candidate is found. Indiana University is an equal opportunity/affirmative action employer.

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