- phenixbb - phenix-online.org

phenix.elbow error
by Eugene Osipov 10 Mar '19

10 Mar '19

Dear phenix developers, I have found that QM calculations in phenix.elbow fail due to an error: *bad fp number.* I've found the source of the error in phenix-1.14-3260/modules/elbow/elbow/quantum/run_utils.py at line 11: easy_run.call('./%s.csh >& /dev/null' % project) should be : easy_run.call('./%s.csh 2>&1 /dev/null' % project) Also jaguar template (phenix-1.14-3260/modules/elbow/Jaguar.csh) is a bit outdated. For $SCHRODINGER/jaguar paramether -PROC was replaced by -PARALLEL also, it seems that programs seeks for wrong input file. So I suggest that: $SCHRODINGER/jaguar run -PROCS %d -WAIT $PROJECT should look like: $SCHRODINGER/jaguar run -PARALLEL %d -WAIT $PROJECT.in Can you please fix this issues in next releases? -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2

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Fo-Fo difference map for non-isomorphous datasets
by Jordan Luke Pederick 09 Mar '19

09 Mar '19

Hi, I am trying to generate a Fo-Fo difference map for two data sets of the same protein at ~2.3 angstrom resolution. One dataset is native and the other was soaked with a metal ion, so the purpose of the map is for identifying and visualizing peaks that may correspond to a bound metal ion. These datasets differ by 6 angstroms (~10%) along the A edge - an isomorphous difference map generated in Phenix GUI wasn't useful As an alternative I was planning to make a real-space Fo-Fo difference map making use of Superpose Maps in Phenix Gui as follows: Superpose maps would be used to superimpose (Fobs.metal, PHI.metal) and (Fobs.native, PHI.native) The superimposed maps will be opened in Coot and a difference map generated using "Extensions -> Maps -> Make a difference map" There were two things I was unsure about: Does this seem like a reasonable alternative? Is scaling of the two datasets required before generating the difference map? Cheers, Jordan

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Units in intensity?
by Murpholino Peligro 09 Mar '19

09 Mar '19

If I do `phenix.xtriage XDS_ASCII.HKL` I get a log file. In the "Statistics for data merging" of this log file I have: Resolution: 26.02 - 1.40 Observations: 44675 Unique reflections: 16306 Redundancy: 2.7 Completeness: 70.37% Mean intensity: 1656.8 Mean I/sigma(I): 19.8 SigI < 0 (rejected): 644 observations R-merge: 0.027 R-meas: 0.032 R-pim: 0.017 My question is... what units does Mean intensity has? Thanks Ps I am not sure if this has to do with the detector used which was a CCD (type) ADSC QUANTUM 210 (model).

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difference in Wilson B calculated in Xtriange or Polygon
by Eze Chivi 08 Mar '19

08 Mar '19

Hi, The value of Wilson B calculated in Phenix differs for the same data when I use Polygon or Xtriange, why? In Xtriange-->Absolute scale and Wilson analysis: ML estimate of overall B value: 48.88 A**2 In Polygon: 52.05 Thank you Ezequiel

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contour values for Polder and FEM
by V F 07 Mar '19

07 Mar '19

Hi all, What is the recommended values for contouring for Polder and FEM? In pymol, I have a isomesh polder_COA_mesh, polder_207_1, 3, select_COA, carve=2 isomesh FEM_COA, fem_coa_190, 1, select_COA, carve=2 Are these sensible values? Many thanks, Vero PS: Both identify ligand very well!

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AUC2019 – registrations are open.
by Renwick Dobson 06 Mar '19

06 Mar '19

Dear Structural Biology community, AUC2019<https://auc2019.uleth.ca/>, the 24th AUC Workshop and Symposium, will be held at the University of Canterbury, Christchurch (New Zealand) from 24-29 August 2019. The format of the event is a 2-3 day workshop<https://auc2019.uleth.ca/workshops.php> offering parallel, hands-on training in experimental design and the latest AUC data analysis software from the world experts in this area followed by a 2 day research symposium on AUC and complementary approaches: methodological development, combination with orthogonal techniques (SAXS, SANS, SPR, MST, SEC-MALLS etc), application in biosciences and material sciences. Registrations are now open and details can be found at this website: https://auc2019.uleth.ca/ As the scientific program<https://auc2019.uleth.ca/symposium.php> for AUC2019 emerges, events will be uploaded to the website. We strongly encourage you to submit abstracts for talks and posters<https://auc2019.uleth.ca/abstracts.php>. The meeting is also timed such that delegates can also attend the Queenstown Molecular Biology Conference<https://www.queenstownresearchweek.org/> (which is in Queenstown), although note that this is a separate conference. Lastly, The European Biophysics Journal has kindly agreed to run a special issue to celebrate the research presented at AUC2019. Therefore, we invite those who wish to extend their talks to a journal publication to consider contributing original research articles to this issue. Please indicate your interest for inclusion in this volume below. Deadline for registration of a contribution is August 30 2019. We look forward to welcoming you to Christchurch, New Zealand next Spring(-ish)! Ren Dobson, Chair AUC2019 On behalf of the AUC2019 Scientific Organising Committee ---- Prof. Ren Dobson Co-Director, Biomolecular Interaction Centre (BIC) http://www.bic.canterbury.ac.nz/ School of Biological Sciences | Te Kura Pūtaiao Koiora University of Canterbury | Te Whare Wānanga o Waitaha Private Bag 4800 Christchurch | Ōtautahi New Zealand | Aotearoa E: renwick.dobson(a)canterbury.ac.nz<mailto:[email protected]> T: ++64 (03) 369-5145 x 95145 F: ++64 (03) 364-2590 W: http://dobsonlab.org/

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Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble
by Stephen Cusack 05 Mar '19

05 Mar '19

Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble We are looking for a highly motivated and ambitious individual to progress our understanding of the mechanism of transcription by influenza virus RNA-dependent RNA polymerase. The work is in the frame of the ANR-funded FluTranscript project that brings together the complementary expertise of the groups of Stephen Cusack (EMBL Grenoble, project coordinator) and Nadia Naffakh (Institut Pasteur) in structural biology and molecular virology, respectively. The project follows on from a recent joint publication (Structural basis of an essential interaction between influenza polymerase and Pol II CTD. Lukarska et al, Nature 2017) and aims to reconstitute and determine the structure of functional transcription complexes. A secondary goal is to use the acquired structural information to develop new approaches to anti-influenza drug development. The Cusack group uses X-ray crystallography and cryo electron-microscopy to study the structural biology of protein-RNA complexes involved in RNA virus replication, innate immunity and cellular RNA metabolism. Group website: https://www.embl.fr/research/unit/cusack/index.html The successful candidate should have a PhD in Molecular Biology or related field and a strong background and interest in biochemistry and structural biology. We are looking for a creative and ambitious person with good communication skills and keen to work on a challenging project. Experience in insect cell expression systems, reconstitution of protein-RNA complexes, X-ray crystallography or cryo-electron microscopy would be particularly beneficial. EMBL is one of the world’s leading research organizations in the life sciences. The Headquarters Laboratory is located in Heidelberg, with additional sites in Barcelona, Grenoble, Hamburg, Hinxton, and Rome. EMBL Grenoble has excellent access to state-of-the-art structural biology technologies with the in house EM facility being equipped with a T12 microscope and 200kV Glacios/Falcon III . Additionally, we have access to the Titan Krios at the adjacent ESRF as well as those in EMBL Heidelberg. Other facilities on the Grenoble Campus include the ESRF synchrotron X-ray beamlines, neutron scattering at the ILL, high-field NMR at the IBS as well as high-throughput crystallization platform, mammalian and insect cell facilities, biophysical platform and confocal microscopy. You can find out more about this vacancy at: https://www.embl.fr/jobs/searchjobs/index.php?ref=GR00133 or by contacting Stephen Cusack: cusack(a)embl.fr Please apply online through www.embl.org/ Stephen Cusack -- ********************************************************************** Dr. Stephen Cusack, FRS Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL) Group leader in structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

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Are TLS parameters applied when TLS refinement is OFF?
by Mark Saper 04 Mar '19

04 Mar '19

I have a structure where at one stage TLS parameters were determined and then refined. It caused the R-free to increase so I stopped refining the TLS parameters. Are the TLS parameters still applied to the structure on subsequent refinement runs even when the TLS refinement is off? Is it appropriate to refine anisotropic B’s for a high resolution (1.35 Å) structure AND apply TLS parameters? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353 mobile: (734) 276-6505

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MAD merged dataset deposition
by Eugene Osipov 03 Mar '19

03 Mar '19

Hello, everyone, I have solved the structure of heme containing protein using anomalous signal from Fe atom (~1.739 anstroms) and further refined it using native dataset (0.9 angstroms). Structure was solved in AutoSol. The question is "What is the best way to deposit mtz with both datasets?" Should I merge and scale them simultaneously or can I deposit output file from AutoSol overall_best_refine_data.mtz, which contains F,FP, Rfree and HL coefficients? P.S.: please, respond in PM, I have only digest subscription on phenixBB. Thank you in advance! -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2

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Rotamer restraints in phenix.real_space_refine
by Ashley Pike 28 Feb '19

28 Feb '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 30 Jan '19

30 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. 28 Jan '19

28 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

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