Re: [ccp4bb] EM maps

Hi, try to keep the default radius of the map reasonably small, e.g. 25 Å, for displaying purposes. Best, Bruno From: CCP4 bulletin board On Behalf Of Dean Derbyshire Sent: vendredi 8 mars 2024 11:48 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] EM maps Hi, I'm almost certain this has been

[ccp4bb] iNEXT-D FIB-Tomo workshop 15-19.4.2024

om/v3/__https:/fibtomo.sciencesconf.org/__;!!Mih3wA!Hi3HCz35SBTrwmT-0W_Gq_9J63jzFRbiA4UGxbOhi5ocn1ucbbnptSvd2h7toONOpv_BqAl5iyxtGwA-F76o$> Best regards, Bruno Klaholz On behalf of the organizing committee Bruno Klaholz (CBI/IGBMC), Simone Mattei (EMBL-HD), Jirka Novacek (CEITEC) and Karen Davi

Re: [ccp4bb] About the A in AI

indeed, probably they are using the same databases and features. Same happens in translations btw. Cheers, Bruno From: CCP4 bulletin board On Behalf Of Ian Tickle Sent: 12 May 2023 17:33 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] About the A in AI Hi Bernhard Methinks there's some cri

Re: [ccp4bb] Rational mutations and crystallizability

maybe this can help too: https://pross.weizmann.ac.il/step/pross-terms https://proteopedia.org/w/Journal:Molecular_Cell:1 best, Bruno ### Bruno P. Klaholz Centre for Integrative Biology Department of Integrated Structura

[ccp4bb] iNEXT-D hands-on workshop on cryo-FIB lamella preparation & cryo electron tomography 17-21.4.2023

om/v3/__https:/inextfibet.sciencesconf.org/__;!!Mih3wA!FM4qVYfkflfNdyPcO9D6KqM5zicve7Axo0RIlBBEUpnv8YaM2osVa6SNVDIi3_8SgscqwZAxyeVUGEvw0m8F$> Best regards, Bruno Klaholz On behalf of the organizing committee Bruno Klaholz (CBI/IGBMC), Julia Mahamid (EMBL-HD), Ludo Renault (NeCEN), Jirka

Re: [ccp4bb] Map superposition!

Hi Rams, did you try to pre-align one map on the other by first moving it manually in chimera (X) and then only use the "fit in" option for automatic alignment? Automatic alignments often don't work from scratch, but if you try different manual prealignments it helps getting out of a local mini

[ccp4bb] Cryo-EM specialist position at CBI / IGBMC, Strasbourg

the ccp4bb/em mailing lists work again ;-) With best regards, Bruno Klaholz Cryo-EM specialist position: The CBI / IGBMC is seeking an experienced cryo-EM scientist to participate in running the cutting-edge EM facilities at the Centre for Integrative Biology (CBI) at IGBMC, Illkirch

[ccp4bb] cryo-EM/cryo-ET access at CBI via iNEXT-Discovery

very.eu/submit-proposal Best regards, Bruno Klaholz Cryo-EM facilities at CBI/IGBMC: The cryo-EM facility has Titan Krios and Glacios cryo electron microscopes for cryo-EM and tomography, cryo-FIB/SEM, super-resolution imaging (dSTORM), and a suite of associated equipments for sample preparation

Re: [ccp4bb] MR solution not working

Hello, are the low resolution data complete? How do the statistics look like (completeness, I/sigma etc.)? Missing low resolution data (e.g. hidden by the beam stop) can create problems in MR. Any axis aligned along the rotation axis by bad luck (would benefit from offset during data collection

[ccp4bb] Joint access call Instruct-ERIC & iNEXT-Discovery

[Instruct-ERIC logo] [Instruct-ERIC] [LinkedIn] [Twitter] Dear All, Recently, the structural biology platforms Instruct-ERIC

[ccp4bb] cryo-EM postdoc position in Klaholz lab CBI / IGBMC, Strasbourg

/postdoctoral-researcher/ http://www.igbmc.fr/igbmc/recrutement/job_offer/524/ https://www.linkedin.com/posts/bruno-klaholz-35893a125_we-have-an-open-position-for-a-post-doctoral-activity-6733065823482646528-tvhP We are studying the structure and function of large nucleoprotein complexes (ribosome

[ccp4bb] Postdoctoral position at CBI / IGBMC, Strasbourg

copy https://emploi.cnrs.fr/Offres/CDD/UMR7104-GUEBUR-009/Default.aspx?lang=EN - engineer or postdoc position for developments in super-resolution microscopy (please contact me if interested) With best regards, Bruno Klaholz For ongoing projects and full publication list of the

[ccp4bb] Cryo-EM beamline scientist permanent position at CBI / IGBMC, Strasbourg

Dear all, here is an announcement for a permanent position as cryo-EM beamline scientist at the Centre for Integrative Biology, Strasbourg, France. Deadline is tomorrow 2.7.2020 12 am CET. With best regards, Bruno Klaholz Cryo-EM beamline scientist (permanent position): The IGBMC/CBI is

Re: [ccp4bb] Wincoot stereo display on Windows 10

Dear Yong, Arne, Eric and others, this seems to be related with Windows 10 indeed, an upgrade of a machine in our lab from Windows 7 to 10 lost the 3D capability. Same now for a laptop running with Windows 10, which is connected to a Zalman monitor (passive stereo with real3D glasses, i.e. Nvid

[ccp4bb] Cryo-EM acces for Covid-19 projects at CBI / IGBMC, Strasbourg

freezing and screening of grids for purified samples. To apply please see below. With best regards, Bruno Klaholz Cryo-EM facilities: The Centre for Integrative Biology (CBI) at IGBMC, Illkirch/Strasbourg, France, provides a cutting-edge scientific and technological environment in integrated

[ccp4bb] Cryo-EM specialist position at CBI / IGBMC, Strasbourg

. Please see below the detailed job description and how to apply. With best regards, Bruno Klaholz Cryo-EM specialist position: The CBI / IGBMC is seeking a highly motivated cryo-EM specialist to join the cutting-edge EM facilities at the Centre for Integrative Biology (CBI) at IGBMC, Illkirch

[ccp4bb] Cryo-EM beamline scientist position at CBI / IGBMC, Strasbourg

Dear all, here is an announcement for a cryo-EM beamline scientist position at the Centre for Integrative Biology, Strasbourg, France. With best regards, Bruno Klaholz Cryo-EM beamline scientist position: The IGBMC/CBI is seeking a experienced scientist to participate in running the

Re: [ccp4bb] Cryo-EM Full Professor position at Strasbourg University

for that if you have an equivalent position elsewhere (e.g. associate professor or full professor in any other University in France or abroad). If you are interested or have questions about the position please write to the contact persons indicated below. Best regards, Bruno Klaholz From

Re: [ccp4bb] Cryo-EM Full Professor position at Strasbourg University

persons indicated below. Best regards, Bruno Klaholz INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY CALL FOR APPLICATIONS FOR A PROFESSOR AND GROUP LEADER POSITION IN MOLECULAR AND CELLULAR CRYO ELECTRON MICROSCOPY A full professor position is open at the Strasbourg University to

Re: [ccp4bb] cryo-EM

Dear Xavier, dear all, good points indeed. I guess the aim is to refine an atomic model against a cryo-EM map so that the atomic model describes the experimental data well, aiming for a good final geometry, refined B-factors etc. of the atomic model. Here is a description of what we recently di

[ccp4bb] Cryo-EM Full Professor position at Strasbourg University

ill be held in May 2019 (Web site for application and details to be announced in January-February 2019). Assistance can be provided by IGBMC administrative services for both steps. Candidates should contact Bruno Klaholz (bruno.klah...@igbmc.fr<mailto:bruno.klah...@igbmc.fr>) (33) 3 69.4

[ccp4bb] Cryo-EM beamline scientist position at CBI / IGBMC, Strasbourg

Dear all, here is an announcement for a cryo-EM beamline scientist position at the Centre for Integrative Biology, Strasbourg, France. With best regards, Bruno Klaholz Cryo-EM beamline scientist position: The IGBMC/CBI is seeking a experienced scientist to participate in running the

[ccp4bb] PhD and postdoctoral position at CBI / IGBMC, Strasbourg

those present at the 3D-EM Gordon conference please feel free to contact me directly. With best regards, Bruno Klaholz Some recent publications: - L. Andronov, J. Michalon, K. Ouararhni, I. Orlov, A. Hamiche, J.-L. Vonesch & B. P. Klaholz. 3DClusterViSu: 3D clustering analysi

Re: [ccp4bb] EM voxel size correction

Dear Reza, you can do this kind of precise magnification calibration by fine-scaling the cryo-EM map with respect to your atomic model using for example Chimera. Try varying the scales by increments of 0.01 of the pixel size and check for the best cross-correlation between the cryo-EM map and

[ccp4bb] Cryo-EM Professor position at Strasbourg University

Dear all, the University of Strasbourg, France, is opening a call for a Professor and group leader position in cryo-EM. Interested applicants please see below for further informations. Best regards, Bruno Klaholz INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY CALL FOR

Re: [ccp4bb] Van der waals force

Hello, van der Waals interactions are very weak, this is why we usually speak about van der Waals contacts rather than interactions. These are usually in the range of 3.5-3.8/4 Å (smaller than that may indicate a close contact or steric clash of an atomic model under refinement), corresponding

[ccp4bb] postdoctoral position at Centre for Integrative Biology, IGBMC, Strasbourg

, Bruno Klaholz Some recent publications: - I. Orlov, A. G. Myasnikov, L. Andronov, S. K. Natchiar, H. Khatter, B. Beinsteiner, J-F. Ménétret, I. Hazemann, K. Mohideen, K. Tazibt, R. Tabaroni, H. Kratzat, N. Djabeur, T. Bruxelles, F. Raivoniaina, L. di Pompeo, M. Torchy, I. Billas, A

Re: [ccp4bb] Cryo-EM beamline scientist position at CBI, Strasbourg

Dear all, kind reminder for the cryo-EM beamline position at the Centre for Integrative Biology. Application deadline is next week 15.1. Best regards, Bruno Klaholz De : Bruno KLAHOLZ Envoyé : vendredi 9 décembre 2016 17:51 À : CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Dna model

Dear Andy, maybe try GraphiteLifeExplorer which seems convenient for modeling large DNA sequences as well: http://www.lifeexplorer.info/tutorials/ Best, Bruno De : CCP4 bulletin board de la part de Anindito Sen Envoyé : mercredi 21 décembre 2016 07:

[ccp4bb] Cryo-EM beamline scientist position at CBI, Strasbourg

Dear all, here is an announcement for a cryo-EM beamline scientist position at the Centre for Integrative Biology, Strasbourg, France. With best regards, Bruno Klaholz Cryo-EM beamline scientist position: The IGBMC/CBI is seeking a experienced scientist to run the cutting-edge EM

[ccp4bb] IGBMC call for Group Leader positions in Integrated Structural Biology

Dear all, I would like to draw your attention to the opening of two Group leader positions in the Integrated Structural Biology (ISB) department of the Institute of Genetics and Molecular and Cellular Biology (IGBMC) in Illkirch, France (http://www.igbmc.fr/research/department/3/). Detailed in

Re: [ccp4bb] Why the phases from sftools are flipped?

Dear Steven, maybe you have to permutate the order in the way the map is read in, here is what I have used some time ago for an EM map. HTH, best regards, Bruno /usr/local/rave/rave_linux/lx_mapman < set spacegroup > P1 > set cell > 200 200 200 90.00090.00090.000 > mapin input.map

[ccp4bb] deadline for applications to the Meeting on “Current Challenges in Integrated Structural Biology” 19/20 June 2014, Strasbourg

submission. Registration is open up to June 8th. Best regards, Bruno Klaholz Confirmed speakers: - Frédéric Allain, ETH Zürich, Switzerland. Using NMR and EPR to decipher the molecular mechanisms of translation regulation. - Xavier Darzacq, ENS, Paris, France. Single molecule, high

[ccp4bb] Integrated Structural Biology, PhD program at the IGBMC

teams of the Integrated Structural Biology department at http://www.igbmc.fr/research/department/3/ Please feel free to contact the group leaders for further information about the projects. Best regards, Bruno Klaholz

[ccp4bb] Meeting on “Current Challenges in Integrated Structural Biology” 19/20 June 2014, Strasbourg

). Seehttp://ccisb2014.sciencesconf.org/ for registration and a detailed description of the meeting. Application deadline is May 25th 2014, registration is limited to about 100 people and will be processed on a first-comes-first basis. Best regards, Bruno Klaholz

[ccp4bb] international PhD program at IGBMC, deadline for application 22.3.2013

Dear all, kind reminder for the International PhD program at the IGBMC, notably for integrated structural biology, with a deadline for applications 22nd of march 2013: http://phdprogramme.igbmc.fr/ see also http://www.igbmc.fr/research/department/3/ Best regards, Bruno Klaholz

[ccp4bb] Workshop "Computational challenges in Structural Biology" Strasbourg November 14 & 15 2012

Workshop "Computational challenges in Structural Biology" Strasbourg November 14 & 15 2012. See web site : http://ccsb2012.loria.fr/ This mail is to announce the forthcoming workshop "Computational challenges in Structural Biology" which will be held in Strasbourg November 14 & 15 2012.The mai

Re: [ccp4bb] Rigid body refinement with phenix using EM maps.

m not sure if this is the case but Phenix reads columns 1 and 2 as "Map coefs". Do you have any clue? Best regards, Wojtek On 07/13/2012 05:53 PM, Bruno KLAHOLZ wrote: > Dear Wojtek, > > you can try something of this type to get the EM map converted into an hkl > list and mt

Re: [ccp4bb] Rigid body refinement with phenix using EM maps.

Dear Wojtek, you can try something of this type to get the EM map converted into an hkl list and mtz file with I's and some sigma I's estimated to 1/10 of the I's (the latter is required for running fittings/refinements etc.). Best, Bruno /usr/local/rave/rave_linux/lx_mapman

[ccp4bb] Deadline april 16th: 24/25 May 2012 IGBMC symposium on “Future Challenges in Integrative Structural Biology”

. Yannick Schwab, IGBMC, Correlative Light and Electron Microscopy: from living Specimen to 3D Ultrastructure. Olivier Poch, IGBMC, Information Universe for in silico macromolecular Complex Reconstruction. Bruno Klaholz, IGBMC, Challenges in multi-resolution Integration: Structure of DNA-bound full

[ccp4bb] 24/25 May 2012 IGBMC symposium on “Future Challenges in Integrative Structural Biology”

complexes, exemplified by viruses. Best regards, Bruno Klaholz De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]<mailto:[mailto:CCP4BB@JISCMAIL.AC.UK]> De la part de Bruno KLAHOLZ Envoyé : Thursday, March 01, 2012 7:26 AM À : CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.

[ccp4bb] 24/25 May 2012 IGBMC symposium on “Future Challenges in Integrative Structural Biology”

9th 2012, but registration is limited to about 100 people and will be processed on a first-comes-first basis. Best regards, Bruno Klaholz ### Dr. Bruno P. Klaholz Department of Integrated Structural Biology Institute

Re: [ccp4bb] Displaying CH---N weak hydrogen bonds

Dear Rex, if you display hydrogens in Pymol you should be able to draw distances between any atoms (select the 2 atoms of interest with Ctrl + middle mouse, and type "distance" into the command line). However, one should obviously keep in mind the geometry of the free electron pairs to which H

Re: [ccp4bb] Ice rings...

Dear Francis, the spots will be excluded individually based on the inhomogeneous background, so you don't need to apply a resolution cutoff. However, once you have determined and refined your structure it may be worth predicting the intensity of these spots and put them back for map calculation,

Re: [ccp4bb] How to labe the stereo-view figs?

Dear Yuan, it depends which software you are using, usually it is not so convenient to add labels with good font sizes, colors etc. So the way I do it is to put the 2 pictures next to each other in powerpoint (at good resolution, e.g. A3 format), add labels on the one on the left in text mode,

Re: [ccp4bb] Importance of low order reflections?

Dear Richard, the low resolution reflections are important for any data set, whether this is a high or medium resolution data set: they describe features corresponding to the size and global position of the crystallized molecule. That's why they are important for molecular replacement, for l

Re: [ccp4bb] Back-Fourier transforming an EM map with SFALL

Dear Larry, you may have to coarsen and cut your map into 120,120,120 (full sampling may not be needed anyway for MR) or try cutting into 240,240,240 (though I haven't tried such big values yet). I noticed that you have already converted the axes to XYZ (I guess with the uvw option in mapman)

Re: [ccp4bb] Fancy crystal, poor diffraction

Dear Tiancen, I would suggest to try optimizing the hydration state of the crystal. Either with a humidity controller (e.g. FMS system) at room temperature (or 4 degrees), with which you can optimize the diffraction, or by partially drying the crystal on a filter paper soaked with some precipit