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LISTSERV Web Interface 16.52024-03-19T07:35:19Zzx2020@connect.hku.hk2024-03-19T07:35:08+00:002024-03-19T07:35:08+00:00Running Crank2 via Command Linehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;aed1cdcc.2403Hello everyone,<br><br>I'm reaching out to inquire if anyone has experience with executing Crank2 through the command line. I attempted utilizing the crank command, but it appears an XML input is required. To generate the XML file, I employed gcx with the following parameters:<br><br>gcx SEQIN /mnt/ssd/SAD/5uxx/rcsb_pdb_5UXX.fasta << END<br>XTAL DEFAULT<br>ATOM Se<br>DNAM PEAK<br>MTZI /mnt/ssd/SAD/5uxx/AUTOMATIC_DEFAULT_free.mtz<br>outp gcx<br>END [...] Andriy Kryshtafovych2024-03-18T18:16:33-07:002024-03-18T18:16:33-07:00Call for targets for the 2024 CASP modeling experimenthttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;fc54a9fa.2403CASP (Critical Assessment of Structure Prediction) experiments are held<br>every two years. Recent rounds have seen dramatic increases in modeling<br>accuracy, resulting from the introduction of deep learning methods: In<br>2018, for the first time, the folds of most proteins were correctly<br>computed [1]; in 2020, the accuracy of many computed protein structures<br>rivaled that of the corresponding experimental ones [2]; in 2022, there<br>was an enormous increase in the accuracy of protein complexes [3]. [...]Stojanoff, Vivian2024-03-18T23:44:37+00:002024-03-18T23:44:37+00:00Reminder: CBMS Lecture Series; Dessen, March 20.https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;da2eb988.2403You are cordially invited to join the Center for Biomolecular Structure Lecture Series ………..<br><br>Andrea Dessen<br><br>CNRS Research Director<br><br>Institut de Biologie Structurale, France<br><br>WEDNESDAY, March 20, 13:30 (EDT)<br><br>"Architecture and Genomic Arrangement of Bacterial Cell Biosynthesis Complexes"<br><br>Register in advance for this meeting:<br><br>https://bnl.zoomgov.com/meeting/register/vJIsdOysqzoiHJzcKLSKZqX5jfwZQcIozkM<br><br> Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https://gcc02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.worldtimebuddy.com*2F&data=05*7C01*7Cgenoa.blankenship*40pnnl.gov*7C67ffe754733240e42d3e08da641ba4bc*7Cd6faa5f90ae240338c0130048a38deeb*7C0*7C0*7C637932367171794987*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=aSe2IUSomjge9ZW6zXdQ81fPzxpg8eawtRkoiOEJdXM*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!P4SdNyxKAPE!Fd5kIAbibocFpkUaEbpqZZGm8tw-xiqb5oC4sfOklv6Kbbf-T3RvUobMSLrzyXNbfNVT9vMxJGuY1RsSqbc6MjpIABre1Q$><br><br>Abstract: The bacterial cell wall is important for survival and shape, and its biosynthetic mechanism is the target of beta-lactam antibiotics. The spread of resistant strains, however, has limited the usefulness of these drugs and calls for efforts towards studies of cell wall formation that could lead to the development of [...]Paul Emsley2024-03-18T16:07:02+00:002024-03-18T16:07:02+00:00Re: Coot function - closest symmetry atom?https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;efa96264.2403On 18/03/2024 10:26, Petr Pachl wrote:<br>> --<br>><br>><br>> Does anybody know if there is a function (or procedure) how to get info<br>> about closest symmetry atom? For picking coot is performing something<br>> like "Model atom pick (if failed) -> Symmetry atom pick", then it<br>> returns to console and atom info at the bottom of the screen the found<br>> atom. But can that be obtained in a function? My idea is to have a<br>> shortcut "go to original atom based on symmetry related one". [...]Carlos CONTRERAS-MARTEL2024-03-18T13:18:37+01:002024-03-18T13:18:37+01:002-year postdoctoral positio IBS Grenoble-Francehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;c39899cf.2403Researcher in structural biology (w/m)<br><br>We have a funded 2-year postdoctoral position available in the<br>Metalloproteins Unit at "Institut de biologie Structurale" (IBS) in<br>Grenoble. The research will focus on the structural study of iron-sulfur<br>(Fe-S) cluster biosynthesis in both prokaryotes and eukaryotes.<br><br>We are looking for a candidate with a Ph.D. in structural biology<br>obtained less than 2 years ago, and proficiency in state-of-the-art<br>cryoEM or X-ray crystallography software and techniques. More<br>information about the position can be found here: [...]Petr Pachl2024-03-18T11:26:06+01:002024-03-18T11:26:06+01:00Coot function - closest symmetry atom?https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;79a4d954.2403Hi all.<br>Does anybody know if there is a function (or procedure) how to get info<br>about closest symmetry atom? For picking coot is performing something<br>like "Model atom pick (if failed) -> Symmetry atom pick", then it<br>returns to console and atom info at the bottom of the screen the found<br>atom. But can that be obtained in a function? My idea is to have a<br>shortcut "go to original atom based on symmetry related one". [...]Carlos CONTRERAS-MARTEL2024-03-18T11:14:42+01:002024-03-18T11:14:42+01:002-year postdoctoral position in crystallography at IBS/METALLO Grenoblehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;2bda76bd.24032-year postdoctoral position in crystallography at IBS/METALLO Grenoble<br><br>A postdoctoral position in Structural Biology is available in the<br>Metalloproteins group at IBS in Grenoble, France. This position focuses<br>on trapping and structurally characterizing reactive intermediates in<br>the time course of Radical SAM enzymes. Led by Yvain Nicolet, the group<br>is seeking a highly motivated candidate with experience in protein<br>expression, purification, and crystallization. A solid background in<br>X-ray crystallography is desirable, as is an affinity for using computer<br>tools, including basic programming skills for a better utilization of<br>the software dedicated to structural data processing and analysis.<br>Application deadline *May [...]Stojanoff, Vivian2024-03-15T21:26:19+00:002024-03-15T21:26:19+00:00CBMS Lecture Series - Andrea Dessen - March 20https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;42c5b368.2403You are cordially invited to join the Center for Biomolecular Structure Lecture Series ………..<br><br>Andrea Dessen<br><br>CNRS Research Director<br><br>Institut de Biologie Structurale, France<br><br>WEDNESDAY, March 20, 13:30 (EDT)<br><br>"Architecture and Genomic Arrangement of Bacterial Cell Biosynthesis Complexes"<br><br>Register in advance for this meeting:<br><br>https://bnl.zoomgov.com/meeting/register/vJIsdOysqzoiHJzcKLSKZqX5jfwZQcIozkM<br><br> Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https://gcc02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.worldtimebuddy.com*2F&data=05*7C01*7Cgenoa.blankenship*40pnnl.gov*7C67ffe754733240e42d3e08da641ba4bc*7Cd6faa5f90ae240338c0130048a38deeb*7C0*7C0*7C637932367171794987*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=aSe2IUSomjge9ZW6zXdQ81fPzxpg8eawtRkoiOEJdXM*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!P4SdNyxKAPE!Fd5kIAbibocFpkUaEbpqZZGm8tw-xiqb5oC4sfOklv6Kbbf-T3RvUobMSLrzyXNbfNVT9vMxJGuY1RsSqbc6MjpIABre1Q$><br><br>Abstract: The bacterial cell wall is important for survival and shape, and its biosynthetic mechanism is the target of beta-lactam antibiotics. The spread of resistant strains, however, has limited the usefulness of these drugs and calls for efforts towards studies of cell wall formation that could lead to the development of [...]Ankita Punetha2024-03-15T12:27:23-04:002024-03-15T12:27:23-04:00Postdoctoral Fellow position in Membrane Protein Biochemistry and Cryo-EMhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;4a3bb59a.2403Dear Colleagues,<br><br>A postdoctoral fellow position is available in the Petrou lab at Rutgers<br>New Jersey Medical School (NJMS) to support NIH-funded research. Our<br>research focuses on the structural biology of membrane (and soluble)<br>proteins using single particle cryo-electron microscopy (cryo-EM).<br><br>The Postdoctoral Fellow will be responsible for the expression and<br>purification of proteins using bacterial, insect and mammalian heterologous<br>expression systems, and for the structure determination of membrane<br>proteins and/or protein complexes by single-particle cryo-EM. In addition,<br>the Postdoctoral Fellow will be responsible for biophysical and biochemical<br>characterization of target proteins, including protein-ligand or<br>protein-protein interactions. [...]Ankita Punetha2024-03-15T12:18:39-04:002024-03-15T12:18:39-04:00Postdoctoral fellow position is available in the Petrou lab at Rutgers New Jersey Medical Schoolhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;a344e781.2403Dear Colleagues,<br><br>A postdoctoral fellow position is available in the Petrou lab at Rutgers<br>New Jersey Medical School (NJMS) to support NIH-funded research. Our<br>research focuses on the structural biology of membrane (and soluble)<br>proteins using single particle cryo-electron microscopy (cryo-EM).<br><br>The Postdoctoral Fellow will be responsible for the expression and<br>purification of proteins using bacterial, insect and mammalian heterologous<br>expression systems, and for the structure determination of membrane<br>proteins and/or protein complexes by single-particle cryo-EM. In addition,<br>the Postdoctoral Fellow will be responsible for biophysical and biochemical<br>characterization of target proteins, including protein-ligand or<br>protein-protein interactions. [...]Robbie Joosten2024-03-15T10:09:02+01:002024-03-15T10:09:02+01:00Re: isymop reference for ISYM column in MTZ fileshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;8a94a2ac.2403Full message available at: <a href="https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;8a94a2ac.2403">Re: isymop reference for ISYM column in MTZ files</a>David FLOT2024-03-15T10:04:07+01:002024-03-15T10:04:07+01:00Sixth ESRF-INSTRUCT workshop on sample preparation for cryo-EM, May 28-30, 2024https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;b8157745.2403Dear colleague,<br><br>We are pleased to announce the sixth practical hands-on workshop on<br>sample preparation for cryo-EM single particle data collection, jointly<br>organized by the ESRF, EMBL Grenoble, and the IBS, continuing a series<br>started in 2018. This 2.5 day workshop is aimed at PhDs, Postdocs and<br>young scientists new to the field of single particle cryo-EM and will be<br>held at the European Photon Neutron campus, Grenoble, France from M*ay<br>28^th to 30^th , 2024*. The course offers theoretical and practical<br>aspects of sample preparation for single particle cryo-EM including<br>prior quality control by negative staining. The participants will [...]Rangana Warshamanage2024-03-15T08:36:34+00:002024-03-15T08:36:34+00:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;900a821b.2403The line causing troubles is SFAC, I think<br><br>On Thu, 14 Mar 2024, 22:44 Navdeep Sidhu, <sidhun@gmail.com> wrote:<br><br>> Dear Fred,<br>><br>> I hope you'd agree that another good way to bypass similar issues is<br>> that before working on data where you don't know the model, you try out<br>> data where you do. And so I'd recommend this book, which provides you<br>> with practice data and great worked tutorials:<br>><br>> Peter Müller (Ed.). Crystal Structure Refinement: A Crystallographer's<br>> Guide to SHELXL. IUCr/Oxford, 2006<br>> <https://global.oup.com/booksites/content/9780198570769/>.<br>><br>> The book uses XP for visualization (which [...]Hekstra, Doeke Romke2024-03-15T03:59:42+00:002024-03-15T03:59:42+00:00isymop reference for ISYM column in MTZ fileshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;e3e4f7a5.2403Hi,<br><br>I would like to be sure about which symmetry operation the M/ISYM column in an MTZ file is referring to. Is it correct that this matches the order in CCP4's /lib/data/syminfo.lib (at least when this order is unique-it is not always so)? Would anyone know why the order in one of my favorite websites (http://img.chem.ucl.ac.uk/sgp/large/sgp.htm) happens to often be different? [...] Navdeep Sidhu2024-03-14T23:43:50+01:002024-03-14T23:43:50+01:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;6cc307f7.2403Dear Fred,<br><br>I hope you'd agree that another good way to bypass similar issues is<br>that before working on data where you don't know the model, you try out<br>data where you do. And so I'd recommend this book, which provides you<br>with practice data and great worked tutorials:<br><br>Peter Müller (Ed.). Crystal Structure Refinement: A Crystallographer's<br>Guide to SHELXL. IUCr/Oxford, 2006<br><https://global.oup.com/booksites/content/9780198570769/>. [...]Orville, Allen (DLSLtd,RAL,LSCI)2024-03-14T14:30:07+00:002024-03-14T14:30:07+00:00Postdoc position in the XFEL Hub at Diamond Light Sourcehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;690c4caa.2403Hi,<br><br>The XFEL Hub at Diamond Light Source in Oxfordshire UK, has a Postdoctoral Research Associate position open (three years duration) to address time-resolved, dynamic structural biology. We are eager to work with you on serial crystallography correlated with X-ray emission spectroscopy with applications and data collected at Diamond and at XFELs, including SwissFEL. [...] Deborah Harrus2024-03-14T12:08:12+00:002024-03-14T12:08:12+00:00New, free online AlphaFold training coursehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;df58e1a1.2403Dear all,<br><br>Recognising the transformative impact of AlphaFold on scientific<br>research, EMBL-EBI and Google DeepMind have co-developed a comprehensive<br>online training course to facilitate the wider adoption and responsible<br>use of this technology.<br><br>The training course, launched last week offers an interactive learning<br>experience tailored to different levels of expertise. It enables users<br>to delve into the fundamentals of AlphaFold, explore its strengths and<br>limitations, and gain practical skills through hands-on exercises. [...]Deborah Harrus2024-03-14T09:36:13+00:002024-03-14T09:36:13+00:00wwPDB News: CryoEM Archiving and Validation Recommendationshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;32249e6.2403Dear all,<br><br>A workshop was held at EMBL-EBI (Hinxton, UK) in January 2020 to discuss<br>data requirements for deposition and validation of cryoEM structures,<br>with a focus on single-particle analysis and setting community<br>recommendations.<br><br>The outcomes of this meeting have now been published in this manuscript<br>which highlights the recent achievements made by the wwPDB in the space<br>of 3DEM validation and the community recommendations going forward. [...]Clemens Grimm2024-03-14T09:34:44+00:002024-03-14T09:34:44+00:00Open positions for one Postdoc and one PhD studenthttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;f61de9b7.2403Dear All,<br><br>Two research positions funded by the VolkswagenStiftung are available in the group of Prof. Utz Fischer at the Theodor-Boveri Institute of the Julius-Maximilians-Universität Würzburg.<br><br>The successful candidates will participate in a structure-based drug design approach to combat the zoonotic risk imposed by poxviral reservoirs and human pathogenic poxvirus strains. To this end, we target the unique poxviral transcription machinery, which relies exclusively on virus-encoded proteins. As a basis, we recently reported the isolation and comprehensive structural investigation of this machinery in different phases of action. This now enables the identification and design of small molecules that interfere with [...] Jan Dohnalek2024-03-14T08:51:33+01:002024-03-14T08:51:33+01:00School on Single molecule biophysics in cell lysates, 13-17 May 2024, IBT, Vestec, Czech Republichttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;7f4da055.2403Dear colleagues,<br><br>We welcome registrations to a specialized course focused on<br>*Single molecule biophysics*<br>Find all the relevant details on this page<br>https://www.mosbri.eu/training/basic-level-schools/bls2/<br><br>This basic-level school is aimed at biologists, biophysicists, biochemists,<br>structural biologists, etc., who want to learn a technique enabling high<br>throughput screening for dynamic parameters of biochemical interactions on<br>a single molecule level.<br><br>The deadline for submission of an application to participate in this course<br>is: *31 March 2024*. [...]Christina Zimanyi2024-03-13T19:00:00+00:002024-03-13T19:00:00+00:00CryoEM Current Practices Webinar - 03/28/2024https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;21e80cd.2403Dear all,<br>Please join the NIH Transformative High Resolution CryoEM Program service centers at our next CryoEM Current Practices webinar.<br><br>Time: Thursday, March 28, 2024 at 9 AM pacific / 12 PM eastern time<br>Speaker: Prof. Wolfgang Peti, University of Connecticut Health Center<br><br>Title: Using cryo-EM to understand dynamic interactions<br><br>All are welcome to attend. Registration is at no-cost, but sign-up is required:<br>https://us02web.zoom.us/webinar/register/WN_EZtYSZ2XTfaVPSQyqDFzfQ [...] Deborah Harrus2024-03-13T09:51:08+00:002024-03-13T09:51:08+00:00wwPDB News: Latest Developments on the EMDB Publishedhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;28079994.2403Dear all,<br><br>We are please to announce the publication of this manuscript, addressing<br>the recent developments in the archiving of 3DEM data and the future<br>plans for the EMDB.<br><br>The burgeoning popularity of the electron microscopy field has been<br>coupled with new technologies and software solutions, together this has<br>pushed exponential growth in yearly depositions, increases in the<br>resolution of the deposited data, and, consequently, accuracy of<br>molecule models associated with 3DEM data. [...]Elke De Zitter2024-03-13T09:32:40+01:002024-03-13T09:32:40+01:00Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoblehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;7a578b33.2403Dear all, <br> <br>We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The project focuses on the development and optimization of bio-scavengers targeting toxic organophosphorus compounds. The successful candidate will employ time-resolved crystallography and in silico protein design methodologies. The 2-year postdoctoral position is funded by the French National Research Agency via the University Grenoble Alpes, and is open for a young researcher. <br> <br>Applicants must have obtained a Ph.D. in structural biology, biochemistry, biophysics, physics, chemistry, or a related field, no more [...]Mickey Kosloff2024-03-12T18:59:03+02:002024-03-12T18:59:03+02:00Postdoctoral position - computational studies of antibody stability and specificityhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;afc3599.2403We are opening a postdoc position at the Department of Human Biology at the<br>University of Haifa, focusing on the interface of two fields –<br>computational structural biology (of antibodies) and B cell population and<br>genetic analysis. The position can start as early as April 2024, and will<br>be for one year, with an option to extend for at least another year. [...]Tim Gruene2024-03-12T17:54:15+01:002024-03-12T17:54:15+01:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;bcc0a5bb.2403Hi Fred,<br><br>You can place the SHELXL binary anywhere, but you need to tell OLEX2,<br>e.g. by modifying the PATH-variable (search for 'ENVIRONMENT' in the<br>WINDOWS search field. The current working directory (CWD) is part of<br>the PATH in Windows by default, hence by copying shelxl.exe to where<br>you installed the olex2-binary is also a solution, but in case you need<br>shelxl.exe for several programs, the PATH variable but circumvent that<br>you need to copy shelxl.exe in all the different directories one by one. [...]Frederic Vellieux2024-03-12T16:42:16+01:002024-03-12T16:42:16+01:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;3d5b89b1.2403Hi,<br><br>In fact the problem was solved with the help of Ivica Dilovic from<br>Zagreb who suggested some changes to the shelxl .ins file. After these<br>modifications the cryptic error message was still there, but the<br>modifications made me try to remove one card. That did it.<br><br>So the part that is concerned with this error in the .ins file is as<br>follows: [...]Kay Diederichs2024-03-12T15:12:52+00:002024-03-12T15:12:52+00:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;ffac9fa.2403Fred,<br><br>nobody would be offended if you'd just post your SHELXL .ins file here; there are enough experienced crystallographers to spot the mistake.<br>Best would be if you could pare it down to small size, but such that it is still reproducible (my own experience is that this almost always makes me find my own mistakes). [...]ccp4mail2024-03-12T13:47:00+00:002024-03-12T13:47:00+00:00Structure Meets Function Webinar #31https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;f8a10c26.2403Dear All,<br><br>Register now for the 31st edition of the Instruct-ERIC Structure Meets Function webinar series, taking place on Zoom, 19 March at 11:00 CET<https://us06web.zoom.us/webinar/register/WN_0ulkqTTORZ2LC7PlDzWv8w#/registration><br><br>Register Here<https://us06web.zoom.us/webinar/register/WN_0ulkqTTORZ2LC7PlDzWv8w><br><br>The latest webinar in the Instruct-ERIC Structure Meets Function series is hosted by Instruct-FR2. The webinar series offers an insight into the very cutting edge of structural biology research, utilising the latest techniques available through Instruct-ERIC facilities and centres. [...]Beale John Henry2024-03-12T12:04:11+00:002024-03-12T12:04:11+00:00Reminder: Deadline for SwissFEL Call for 2024-IIhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;d7c8caa.2403Dear all,<br><br>I brief reminder that the SwissFEL 2024-II period will close on Friday the 15th of March. Should you wish to submit a proposal, now would be an admirable time to do so.<br><br>Please consult the following website to obtain general information about the call, the status of the available instruments, and the offered setups: https://www.psi.ch/swissfel/calls Tim Gruene2024-03-12T12:13:54+01:002024-03-12T12:13:54+01:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;8d1c6141.2403Dear Fred,<br><br>there is a Bruker mailing list (bruker-axs@g-groups.wisc.edu), that<br>acts as a ccp4bb for small molecule crystallography.<br>As far as I know, there is no automatic inscription, and you should<br>write to Ilia Guzei <iguzei@chem.wisc.edu><br><br>It is good you are on linux, that's one thing less to worry about.<br>If you want to use SHELXL with Olex2, you need to add SHELXL to your<br>PATH environment, either in a terminal from which you start Olex2, or<br>into the 'start' script for Olex2. In SHELXLE, you can add the SHELXL<br>command from the last menu item in the menu 'SHELX' [...] Harry Powell2024-03-12T11:02:35+00:002024-03-12T11:02:35+00:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;8f3653b2.2403Hi Fred<br><br>There *used* to be CCP14 (for small molecules and powders), but this lost funding many years ago.<br><br>In the UK, I’d contact the National Crystallography Service at Southampton to see if they have any pointers to bulletin boards - I have a vague recollection of one but can’t remember the details. Simon Coles is in charge there and may be able to help. [...]Andy Purkiss2024-03-12T10:07:19+00:002024-03-12T10:07:19+00:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;9d719d16.2403Dear Fred,<br><br>You need to register for the Windows (and other OS) installers if you want the stand-alone version of Shelx.<br><br>The form is at https://shelx.uni-goettingen.de/register.php<br><br>We have it running on Windows, although this version came with our Bruker X-ray generator.<br><br>Hope this helps,<br><br>Andy Fred Vellieux2024-03-12T11:03:48+01:002024-03-12T11:03:48+01:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;c5865664.2403Hello again,<br><br>I'll try ccp4 for Windows when I am back at home (where Windows "lives"<br>in my case).<br><br>I have certainly tried shelxle. If I remember well what is provided is a<br>.deb file. I used alien to convert that to a .rpm file, and installation<br>failed because of issues I can't remember (the Linux flavour here is<br>Alma Linux 9, not Debian). [...]David Waterman2024-03-12T09:56:22+00:002024-03-12T09:56:22+00:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;35ed11b5.2403Hi Fred,<br><br>CCP4 distributes the shelxl binary on Linux. I've not checked yet, but<br>perhaps it is also part of CCP4 on Windows?<br><br>Cheers<br>-- David<br><br>On Tue, 12 Mar 2024 at 09:38, Fred Vellieux <frederic.vellieux@lf1.cuni.cz><br>wrote:<br><br>> Hello and thanks for the reply.<br>><br>> My input file came from my checking SHELX manuals and SHELX instructions<br>> on the web, and trying to modify them to suit my case.<br>><br>> I tried olex2 on a Windows computer (somehow olex2 did not run on my Linux<br>> box, and only v1.3 was able to install on that Windows [...]Fred Vellieux2024-03-12T10:38:04+01:002024-03-12T10:38:04+01:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;331447ae.2403Hello and thanks for the reply.<br><br>My input file came from my checking SHELX manuals and SHELX instructions<br>on the web, and trying to modify them to suit my case.<br><br>I tried olex2 on a Windows computer (somehow olex2 did not run on my<br>Linux box, and only v1.3 was able to install on that Windows machine and<br>not the latest v1.5). However, olex2 (the installation program) does not<br>come with Shelx program executables, and I could not locate the<br>installers for the shelx software on Windows. [...]David Waterman2024-03-12T09:12:43+00:002024-03-12T09:12:43+00:00Re: Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;ddeffbc1.2403Hi Fred,<br><br>I find Olex2 and shelxle are both convenient interfaces to SHELXL<br>refinement, that take care of some of the details of .ins file format for<br>you. However, maybe you are stuck in the starting gate, depending on what<br>is malformed in your input file. Where did your input files come from?<br><br>Cheers<br>-- David [...]Fred Vellieux2024-03-12T10:00:36+01:002024-03-12T10:00:36+01:00Is there a bulletin board (similar to ccp4bb) for small molecule crystallographyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;94453adc.2403Hi folks,<br><br>I have a simple question: is there an electronic bulletin board for<br>small-molecule crystallography? I have checked the list of CCP projects<br>and there is no CCP-project for small molecule crystallography in the list.<br><br>I am trying to run SHELXL, and it fails with the cryptic message "** BAD<br>ATOM OR UNKNOWN INSTRUCTION **". [...]Umar Farook2024-03-11T23:33:28+03:002024-03-11T23:33:28+03:00Arpwarp webserverhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;bd3af45c.2403Hello All,<br><br>I have been trying to access the arpwarp web server page for the last 3<br>weeks, but it is not accessible. Does anyone have information on this?<br><br>Thanks in advance!Jonathan Elegheert2024-03-11T12:21:13+01:002024-03-11T12:21:13+01:00Re: EMBO Workshop on Molecular Neurobiology, 13th to 17th May 2024, Cretehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;cab63c77.2403Dear all,<br><br>I would like to re-advertise the EMBO Workshop on Molecular Neurobiology, for which the registration / abstract submission deadline has now been extended to the 18th March.<br><br>https://meetings.embo.org/event/24-mol-neurobiology<br><br>Thank you and best wishes,<br>JonathanTom Burnley - STFC UKRI2024-03-11T10:29:09+00:002024-03-11T10:29:09+00:00Re: Early bird deadline: Monday 11 March - 10th CCP-EM Spring Symposium 30th April - 2nd May 2024https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;b97e668d.2403Hi all,<br><br>Final reminder that earlier bird registration for the Symposium/BCI meeting closes at the end of today (Mon 11 March)<br><br>All the best,<br><br>TomChristine Gee2024-03-08T08:59:21-08:002024-03-08T08:59:21-08:00Re: EM mapshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;10dbde20.2403Hi,<br><br>I had a similar problem with a map crashing coot and pymol while it opened<br>fine in chimera. There was some kind of discrepancy in the file header and<br>the file size (slightly too small), but running through mapmask solved the<br>issue. I can't claim to have figured that out. James Holton showed me the<br>fix. If interested, the mapmask command is echo scale factor 1 | mapmask<br>mapin emdproblemmap.map mapout fixedemdproblemmap.map [...]Paul Emsley2024-03-08T15:52:11+00:002024-03-08T15:52:11+00:00Re: EM mapshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;d0b3e652.2403On 08/03/2024 10:47, Dean Derbyshire wrote:<br>><br>><br>> Hi, I’m almost certain this has been addressed before so apologies…<br>> but is there a trick to import EM map files into COOT, it keeps<br>> crashing when I’ve tried.<br>><br>><br>><br><br>My guess is that your computer is running out of memory. A pint into a<br>quart port? Sometime EM maps can be multi-gigs. And there was a memory<br>leak that I discovered just last week in fact. [...]Sarah Fegan - STFC UKRI2024-03-08T15:02:11+00:002024-03-08T15:02:11+00:00CCPBioSim Industry Talk - Sosei Heptares - 27 March 2024https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;1a35085e.2403Dear all,<br><br>Our next online industry talk is by Brian Bender of Sosei Heptares on 27 March 2024 at 14:00 UK time. Registration is free but required. Details and registration can be found at https://www.ccpbiosim.ac.uk/soseiheptares2024.<br><br>Title: "Applications of AlphaFold and Generative Molecular Design for GPCR SBDD"<br><br>Abstract: Methodologies for structure prediction and molecule design are advancing at a rapid pace. Staying on top of recent developments requires testing them to understand if they are truly useful for prospective research. In this talk, we will explore the uses of AlphaFold and generative molecular design in the context of drug discovery at [...] Tom Burnley - STFC UKRI2024-03-08T13:55:09+00:002024-03-08T13:55:09+00:00Early bird deadline: Monday 11 March - 10th CCP-EM Spring Symposium 30th April - 2nd May 2024https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;300d8e98.2403Hi all,<br><br>Just a reminder that the earlier bird registration for the Symposium closes end of Monday 11th, after than the conference fees will increase:<br><br>Conference fees<br><br>PhD/PDRA Early Bird: £150.00<br><br>Standard Early Bird: £200.00<br><br> <br><br>PhD/PDRA: £200.00<br><br>Standard: £250.00<br><br>Registration page:<br><br>https://cvent.me/Q1QANv<br><br>Please note we have now sold out of our conference accommodation so any new delegates will need to arrange their own accommodation. Hotels are available near the conference centre e.g.: [...]Bruno KLAHOLZ2024-03-08T11:04:57+00:002024-03-08T11:04:57+00:00Re: EM mapshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;570f1115.2403Hi,<br><br>try to keep the default radius of the map reasonably small, e.g. 25 Å, for displaying purposes.<br><br>Best,<br><br>Bruno<br><br>From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Dean Derbyshire<br>Sent: vendredi 8 mars 2024 11:48<br>To: CCP4BB@JISCMAIL.AC.UK<br>Subject: [ccp4bb] EM maps<br><br>Hi, I'm almost certain this has been addressed before so apologies... but is there a trick to import EM map files into COOT, it keeps crashing when I've tried.<br>Ta muchly in advance<br>Dean Dean Derbyshire2024-03-08T10:47:53+00:002024-03-08T10:47:53+00:00EM mapshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;5348bd6b.2403Hi, I'm almost certain this has been addressed before so apologies... but is there a trick to import EM map files into COOT, it keeps crashing when I've tried.<br>Ta muchly in advance<br>Dean Flaig, Ralf (DLSLtd,RAL,LSCI)2024-03-07T17:23:35+00:002024-03-07T17:23:35+00:00PDRA position in structural biology at Diamond Light Source, 3 year fixed term, vacancy closing 10/03/2024https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;3b93c5a9.2403A reminder that this vacancy will be closing on 10/03/2024.<br><br>https://vacancies.diamond.ac.uk/vacancy/postdoctoral-research-associate-structural-biology-502687.html<br><br>We now have an opportunity for an experienced molecular structural biologist, at Post-Doctoral Research Associate level, to further support the structural biology activity<br>on the I04 beamline in the field of chromatin remodelling and histone modification.<br>These projects are pursued as part of the Diamond inhouse research programme and in collaboration with university partners. [...] Diana Tomchick2024-03-07T16:20:22+00:002024-03-07T16:20:22+00:00Re: Mystery blobhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;4d8cc73.2403It’s the Easter Bunny!<br><br>But seriously, it looks like more than one compound, perhaps hydrogen bonded to each other.<br><br>Diana Tomchick<br><br>Sent from my iPhone<br><br>On Mar 7, 2024, at 7:32 AM, Eleanor Dodson <0000176a9d5ebad7-dmarc-request@jiscmail.ac.uk> wrote:<br><br><br>EXTERNAL MAIL<br><br>Anyone ANY idea what this could be?? Beautiful density but...<br><br>I am told:<br>The possible/likely components of the protein solution/cryo/crystallisation buffer are:<br>NaCl, MES, a tiny bit of HEPES possibly, ligand ( GR8.027 = the pentasaccharide near catalytic residues Glu276 and Glu165), Et3N which is monomer TEA (a possible counterion for the ligand - see diagram below), glycerol (cryo)<br>There may also [...]Eleanor Dodson2024-03-07T12:31:38+00:002024-03-07T12:31:38+00:00Mystery blobhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;508bd07c.2403Anyone ANY idea what this could be?? Beautiful density but...<br><br>I am told:<br>The possible/likely components of the protein solution/cryo/crystallisation<br>buffer are:<br>NaCl, MES, a tiny bit of HEPES possibly, ligand ( GR8.027 = the<br>pentasaccharide near catalytic residues Glu276 and Glu165), Et3N which is<br>monomer TEA (a possible counterion for the ligand - see diagram below),<br>glycerol (cryo)<br>There may also be carbonate ions present from the ligand. Any thoughts<br>appreciated!!Gabriel Demo2024-03-07T12:10:29+00:002024-03-07T12:10:29+00:00Postdoc position availablehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;90139c50.2403Dear all,<br><br>We seek a talented individual to fill a postdoctoral position (at the Central European Institute of Technology (CEITEC), Masaryk University Brno, Czech Republic.) with expertise in the field of cryo-electron microscopy and translation regulation. Ideal candidates should possess a solid foundation in biochemistry or structural biology, particularly in single-particle cryo-electron microscopy or protein crystallography. [...] Wolf, Eva2024-03-07T11:49:20+00:002024-03-07T11:49:20+00:00PhD Positions in Mainz/Germanyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;c77bfb8b.2403Dear all,<br><br>2 PhD positions are available immediately in the research group of Eva Wolf in Mainz (Germany). Research in the Wolf group is focused on the structural, biochemical and biophysical analyses of proteins involved in the circadian (day-time dependent) and circalunar (monthly) regulation of cellular, physiological and behavioral processes. We recently described molecular mechanisms and Cryo-EM structures of a marine cryptochrome (L-Cry), which is involved in the synchronization of moon-controlled maturation rhythms of marine worms with the lunar cycle (Pöhn, Krishnan et al, Nat Comm 2022; Vu, Behrmann et al, Nature Comm 2023; Zurl et al, PNAS 2022). The [...] Duncan Johnstone2024-03-07T11:35:50+00:002024-03-07T11:35:50+00:00Data Science Roles @ GSKhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;f0ea4c27.2403Hi,<br><br>We are currently recruiting for two Data Science roles at GSK, which may appeal to individuals with a background in crystallographic software development.<br>These roles are part of a new Data & Predictive Sciences function and in the team that I lead, delivering data science solutions for Target Discovery and Human Genetics & Genomics. [...] Paul Adams2024-03-06T15:44:37-08:002024-03-06T15:44:37-08:00Macromolecular Crystallography - CSHL Course October 2024https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;dc71a217.2403Dear Colleagues,<br><br>The Cold Spring Harbor Macromolecular Crystallography course will take place October 13-29th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher [...] Henry Man2024-03-06T14:36:30+00:002024-03-06T14:36:30+00:00Executive Director, Structural Biology at Exscientiahttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;f55119d8.2403Dear All,<br><br>Exscientia is seeking an Executive Director to lead the Structural Biology team.<br>Please see the full description of the role here: https://apply.workable.com/exscientia/j/98241BEFD6/<br><br>Best Wishes,<br>Henry Man, PhD<br>Senior Crystallographer <br>Exscientia <br>The Schrödinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE<br>The 2023 Prix Galien UK, Best Digital Health Solution<br>The 2022 Prix Galien USA, Best Digital Health Solution<br>Queen’s Award for Enterprise in Innovation 2021Antoine Royant2024-03-06T14:59:41+01:002024-03-06T14:59:41+01:00PhD position in protein crystallography and complementary techniques (ESRF, Grenoble (FR))https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;7fa42294.2403Dear colleagues,<br><br>We have an immediate opening for a PhD position at the ESRF in Grenoble<br>(France) to work mainly on beamline ID30B, at the icOS Lab and at the<br>HPMX Lab in order to study extensively the dynamics of several brightly<br>fluorescent proteins.<br><br>See details and how to apply here:<br>https://esrf.gestmax.eu/1737/1/phd-student-on-id30b/en_US<br><br>Please forward to anyone you think may be interested. [...]Jan Dohnalek2024-03-06T13:08:59+01:002024-03-06T13:08:59+01:00Save the date - Conference Towards Data FAIRness in Molecular Biophysics, Prague 7-8 November 2024https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;345a5d46.2403Dear colleagues,<br><br>We would like to invite you to a conference focused on data management in<br>molecular life sciences.<br><br>*"Towards Data FAIRness in Molecular Biophysics", Institute of<br>Biotechnology, Vestec near Prague, 7-8 November 2024.*<br><br>We would like to bring together people involved in hosting online resources<br>related to molecular<br>biophysics (but also in closely related fields) as well as people doing<br>integrative approaches using online resources. There will be space for<br>discussing interoperability of the existing and emerging repositories and<br>users' views and approach to databases in this field. [...]Sonja Lorenz2024-03-06T09:05:56+01:002024-03-06T09:05:56+01:00PhD and Postdoc positions at the Max Planck Institute in Goettingen/Germanyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;dad68c31.2403Dear colleagues,<br>there are PhD and postdoc positions available in my laboratory at the Max Planck Institute for Multidisciplinary Sciences in Goettingen/Germany.<br>I would be very grateful if you could share the ad and link below with suitable candidates.<br>Link to the job offer:<br>https://www.mpinat.mpg.de/4634381/11-24<br>PhD student or Postdoc (f/m/d)– Specificity mechanisms of ubiquitin ligase complexes –<br>mpinat.mpg.de<br>Many thanks and best wishes,<br>Sonja LorenzEleanor Dodson2024-03-05T15:03:22+00:002024-03-05T15:03:22+00:00Re: mixturehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;265f5514.2403This is best done by calculating the structure factors for the part you<br>want to fix. (make sure the occupancies are set yo 0.8)<br>The REFMAC hklout will contain F SIGF etc plus FCALC PHIcalc for that bit<br>Define this file as your input hkl<br>Then refine the 20% structure (occs=0.2) with input<br>LABI FP=F SIGFP=SIGf FPARTi=FCALC_80% PHIPARTi-PHIC<br>THis will refine the 20% part and add on the structure factors from the 80%<br>without any refinement of that..<br>Eleanor [...]Martin Malý2024-03-05T13:31:53+00:002024-03-05T13:31:53+00:00Re: mixturehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;8ecfadb9.2403Dear Marius,<br><br>could the 'refinement exclude' keyword for refmac5 help?<br>refinement exclude all from [residue] [chain] to [residue] [chain]<br><br>Best regards,<br>Martin<br><br>On Tue, 2024-03-05 at 14:06 +0100, Ilme Schlichting wrote:<br>> Dear Marius,<br>><br>> Thomas discussed this issue in great detail in the supplement of our<br>> recent publication<br>> https://www.nature.com/articles/s41586-024-07032-9<br>><br>> Good luck,<br>><br>> Ilme<br>><br>> On 28/02/2024 17:43, Marius Schmidt wrote:<br>> > Dear All,<br>> > can someone quickly update me with a<br>> > way to refine a mixture of structures in<br>> > refmac or phenix.<br>> > For example, [...]Ilme Schlichting2024-03-05T14:06:39+01:002024-03-05T14:06:39+01:00Re: mixturehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;9d97659e.2403Dear Marius,<br><br>Thomas discussed this issue in great detail in the supplement of our<br>recent publication<br>https://www.nature.com/articles/s41586-024-07032-9<br><br>Good luck,<br><br>Ilme<br><br>On 28/02/2024 17:43, Marius Schmidt wrote:<br>> Dear All,<br>> can someone quickly update me with a<br>> way to refine a mixture of structures in<br>> refmac or phenix.<br>> For example, the mixture consists of<br>> 80 % structure 1 and 20 % structure 2.<br>> It is important that structure 1 is kept<br>> fixed (is not refined) and only structure<br>> 2 is varied.<br>><br>> Best<br>> Marius<br>><br>><br>> Marius Schmidt, Dr. rer. [...]Trevor Forsyth2024-03-05T10:56:17+00:002024-03-05T10:56:17+00:00mRNA therapeutics: postdoctoral position in structural characterization using neutrons, X-rays and electron microscopyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;95c1b13c.2403Understanding mRNA therapeutics: structural characterization using neutrons, X-rays and electron microscopy<br><br>We seek a highly motivated postdoctoral scientist with strong competence in data analysis to carry out structural analyses of a variety of mRNA lipid-based nanoparticles (LNPs) systems using small-angle scattering (SAS) techniques (both neutron and X-ray) alongside cryo-electron microscopy (cryo-EM) studies. The position will be held in the Molecular Biophysics group in the Medical Faculty at Lund University, in close collaboration with CureVac in Germany. [...]Trevor Forsyth2024-03-05T10:45:04+00:002024-03-05T10:45:04+00:00Postdoctoral researcher on transthyretin amyloidosis at Lund University Medical Facultyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;89079676.2403Postdoctoral researcher on transthyretin amyloidosis at Lund University Medical Faculty<br><br>AMBER recruitment call: deadline 18th of March 2024.<br><br>A highly motivated postdoctoral researcher is sought to work on the molecular mechanisms underlying amyloid formation and associated assembly processes. The work will be based in the Molecular Biophysics Group within the Biomedical Center (BMC) at the Faculty of Medicine at Lund University, led by Professor Trevor Forsyth. The major focus of the work will be transthyretin amyloidosis (see https://www.nature.com/articles/s41467-019-08609-z/ ). Human transthyretin (TTR) is a protein that transports thyroxine and retinol-binding protein (RBP) in the serum and cerebrospinal fluid. Wild-type TTR [...]Fearon, Daren (DLSLtd,RAL,LSCI)2024-03-04T15:21:19+00:002024-03-04T15:21:19+00:00PDRA position in antiviral drug discovery at Diamond Light Sourcehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;96c01ec6.2403Dear all,<br><br>We are currently recruiting for a Post-Doctoral Research Associate within the XChem/I04-1 team at Diamond Light Source to drive high-throughput fragment screening experiments and structural biology support for hit-to-lead development as part of our NIH-funded Anti-Viral Drug Discovery Center - the AI-driven, Structure-enabled Antiviral Platform (ASAP). The position is available for the duration of the grant; in the first instance until May 2025. [...] zx2020@connect.hku.hk2024-03-04T13:43:29+00:002024-03-04T13:43:29+00:00Re: i2run crank2 problemhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;82b2364f.2403Dear Stuart,<br><br>Thank you very much for your prompt and helpful response. I apologize for my delayed reply. Your guidance offered a solid foundation, enabling me to successfully implement the procedures you suggested. However, I've encountered additional challenges that were not resolved. Specifically, I need to run the process with the --noDb feature, which operates outside an existing project and generates all output files in the current directory. This requirement continues to pose a problem. [...] Tim Gruene2024-03-04T14:35:39+01:002024-03-04T14:35:39+01:00Re: mixturehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;98e3967.2403Dear Marius,<br><br>it looks like you didn't receive an answer, yet. It would be easy in<br>SHELXL. You may convert the PDB file to the starting instruction<br>filewith PDB2INS.<br><br>Fixing any parameter is done by adding 10 to it, i.e. you can simply<br>run awk on the ins-file to fix x,y,z and Uiso for structure 1, and<br>leave structure 2 to be refined. Actually you would want to add 20 to<br>Uiso and -20 to Uiso for structure 2 in order to refine the fraction of<br>1:2. [...] Gerard Bricogne2024-03-04T12:14:44+00:002024-03-04T12:14:44+00:00Re: Rwork and Rfree the same?https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;67f2cd0e.2403Dear Justin,<br><br>Would it be possible for you to send off-list the report_staraniso.pdf<br>file created by your autoPROC job (or the job number of your STARANISO<br>submission if you used the server) so that we can examine the pattern of<br>data incompleteness indicated by the plots?<br><br>This would be a great help in deciding whether this incompleteness is<br>caused by a missing angular range or purely by anisotropy in the diffraction<br>limits. We would then know what kind of in-filling with Fcalc would occur<br>with what refinement program(s), with what consequences on the maps. [...]Eleanor Dodson2024-03-04T10:46:47+00:002024-03-04T10:46:47+00:00Re: RES: [ccp4bb] Rwork and Rfree the same?https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;738ab96f.2403That is extremely likely! - certainly REFMAC will do that..<br>If 5% missing using DFcalc is a good thing - if 35% is missing not wise..<br>Eleanor<br><br>On Mon, 4 Mar 2024 at 07:53, Ben Bax <ben.d.v.bax@gmail.com> wrote:<br><br>><br>> Fcalc maps look fantastic. Are you sure they were not using an Fcalc for<br>> the missing 35% of the data?<br>> Ben<br>><br>><br>> On 29 Feb 2024, at 21:33, Rafael Marques <rafael_mmsilva@HOTMAIL.COM><br>> wrote:<br>><br>> Sorry for jumping into the post, but I would like the community’s opinion<br>> about completeness, once this topic was raised [...]Ben Bax2024-03-04T07:52:53+00:002024-03-04T07:52:53+00:00Re: RES: [ccp4bb] Rwork and Rfree the same?https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;4fd3a9f5.2403Fcalc maps look fantastic. Are you sure they were not using an Fcalc for the missing 35% of the data?<br>Ben<br><br>On 29 Feb 2024, at 21:33, Rafael Marques <rafael_mmsilva@HOTMAIL.COM> wrote:<br><br>Sorry for jumping into the post, but I would like the community’s opinion about completeness, once this topic was raised here. What could be considered reasonable? Recently I have seen a 65% completeness Crystal structure and, surprisingly, the electron density map was not that bad for a > 3.2 A structure. How such a nice map could have been calculated with such poor parameters? I could only think of [...]Yorgo Modis2024-03-01T14:21:58+00:002024-03-01T14:21:58+00:00Univ. of Cambridge postdoc position at MRC-LMBhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;2109e681.2403Dear CCP4bb list members,<br><br>We are looking for a postdoc with protein biochemistry and cryo-EM experience to join our group to study virus-host interactions. The successful candidate will benefit from an outstanding, supportive environment within the MRC Laboratory of Molecular Biology (LMB) and the University of Cambridge.<br><br>For more details please see:<br>https://www.jobs.cam.ac.uk/job/45467/ <https://www.jobs.cam.ac.uk/job/42215/><br>http://www.mrc-lmb.cam.ac.uk/ymodis/ <http://www.mrc-lmb.cam.ac.uk/ymodis/><br>X: @yorgomodis [...] Bruno KLAHOLZ2024-03-01T06:10:36+00:002024-03-01T06:10:36+00:00iNEXT-D FIB-Tomo workshop 15-19.4.2024https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;c945b806.2403Dear all,<br><br>this is to announce the iNEXT-Discovery one-week hands-on FIB-Tomo workshop on cellular cryo-FIB lamella preparation and cryo electron tomography April 15-19th 2024.<br><br>This is a workshop distributed over four participating centres of the iNEXT-Discovery infrastructure https://inext-discovery.eu<https://urldefense.com/v3/__https:/inext-discovery.eu__;!!Mih3wA!FM4qVYfkflfNdyPcO9D6KqM5zicve7Axo0RIlBBEUpnv8YaM2osVa6SNVDIi3_8SgscqwZAxyeVUGH5aCmG-$>.<br>Practicals will be run in parallel sessions on each site and shared morning lectures on the background and technical aspects will be followed jointly by all the participants.<br>It comprises sample vitrification, cryo-FIB milling to obtain lamella and cryo-ET data acquisition & evaluation. 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