BSI wiki

administrative

Anonymous (anonymous@undisclosed.example.com) — 2023-12-13T10:34:45+00:00

Eurofins Sequencing EVOcard refill Why, when I receive funding from the University of Strasbourg or Inserm, do I have to follow CNRS purchasing procedures?

alphafold

Anonymous (anonymous@undisclosed.example.com) — 2023-11-02T08:22:11+00:00

AlphaFold 2 run on IGBMC HPC Clément script #!/bin/bash #SBATCH --mail-type=ALL #SBATCH --mail-user=charentc@igbmc.fr #SBATCH --cpus-per-task 2 #SBATCH --gres=gpu:a3g.20gb:1 #SBATCH --mem=50G #SBATCH -p gpu module load alphafold/2.3.2 AF=/shared/genomes/alphafold2/2023-04-28 srun run_alphafold.sh \ --data_dir=$AF/ \ --output_dir=$(pwd)/ap_out \ --fasta_paths=Test.fasta \ --max_template_date=2020-05-14 \ --db_preset=full_dbs \ --bfd_database_path=$AF/bfd/bfd_metaclust…

alphafold2

Anonymous (anonymous@undisclosed.example.com) — 2024-03-18T16:04:28+00:00

Using AlphaFold2 on IGBMC HPC * Connect to IGBMC hpc through SSH ssh login@hpc.igbmc.fr * Go to your alphafold folder (/shared/mendel/projects/xxx/cryoem/alphafold/ for instance) * Generate/edit the sequence fasta file (sequence.fasta) >ID_OF_THE_SEQUENCE AMINO_ACID_SEQUENCE

booked

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:46+00:00

Bonjour Luc, L'installation de booked est prête sur la nouvelle VM : Elle s'appuie sur une base MySQL locale pour les données et sur l'AD pour l'authentification des utilisateurs. Tu es administrateur de cette machine (via sudo) et de booked.

borate

Anonymous (anonymous@undisclosed.example.com) — 2024-04-10T15:31:45+00:00

You are a user of TBE buffer We would like to remind you that boric acid and borate have been classified as CMR (Carcinogenic, Mutagenic, Reprotoxic), in this case, toxic for reproduction. Boric acid is one of the components of the TBE (Tris Borate EDTA) buffer, widely used in molecular biology (see attached material safety data sheet). You must wear a lab coat, gloves and safety goggles when handling it.

calculation_servers

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:50+00:00

CBI common calculation servers You can authenticate yourself on the servers directly using your IGBMC credentials, so the username should be the same, and if you had the same password, it will then be transparent for you. If you are outside IGBMC you first need to log to a gateway:

cbi-e2018

Anonymous (anonymous@undisclosed.example.com) — 2024-03-08T16:51:17+00:00

Rules for cell culture room E2018 at CBI Access to the room requires activation of your badge (it takes about a week) and a short introduction by Julien BATISSE. How to book the medium for your production ? The file “Prod Schedule for Media Order_2024” should be filled online (seafile) every time you make production :

cbi-storage_space

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:46+00:00

To transfer your data to the new storage system: It is accessible from the compute and gpu servers at /mnt/storage/teams/ If I did not make any mistake, every project directory that you sent me should be available under: /mnt/storage/teams// If you need to create other project directories, the info I need is in the Data Management Plan. You can now transfer you data from sec-img-data into these project directories.

chimerax

Anonymous (anonymous@undisclosed.example.com) — 2024-02-12T09:10:32+00:00

Using ChimeraX Flip maps with wrong hand Type in the command line : volume flip # or vop zflip # in Chimera Generate Masks

clipping

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:50+00:00

Clipping Procedure source : Before starting * Fill a liquid nitrogen transfer dewars. Make sure it dry before beginning * Assemble the necessary tools: * Flat-T autoloader forceps * C-clip holder wands (one per grid) * Rings and C-clips (one per grid)

cloning

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:56+00:00

Cloning SLIC cloning Mutagenesis GATC sequencing

collected_datasets

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:54+00:00

If you have any data coming from the microscopes, it should be available to transfer from /mnt/gateway/teams/// The best way to transfer it is to use rclone, here is a usage exemple: rclone copy -P -l --transfers=6 /mnt/gateway/teams// /mnt/storage/teams//

common_cryosparc

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:48+00:00

We deployed cryoSPARC on cbi-gpu-03 & cbi-gpu-04 and we are opening the access to everyone. As cryoSPARC is not compatible with the IGBMC authentication system, I have to create the user accounts by hand. To have an account, you have to send an email to CBI-Admins to ask, and you will receive the instance

common_services

Anonymous (anonymous@undisclosed.example.com) — 2024-03-08T15:08:16+00:00

Common services Autoclaves Agarose gels imagers Availability of competent cells on the ISB platform Cell culture facility Rules for cell culture room E2018 at CBI Petits produits Poster printing Referent contact Service missions

competent_cells

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:56+00:00

2023-07-12 Dear all, After getting feedback from the different teams of the ISB department concerning the use of competent cells, specific changes will be made concerning the future availability of these cells on the ISB platform: * Competent cells that are heavily used (TOP10 and BL21[DE3]) will further be provided on the platform (2nd floor, sonication room).

creation_d_une_liaison_arg-ligand

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:54+00:00

Liaison entre ARG et ligand QVR (urgu) * Dans Coot: Calculate, Module... CCP4. Dans l'onglet CCP4, Make Link via Acedrg. Cliquer successivement sur les 2 atomes à lier, ce qui entraîne la création des fichiers acedrg-link-from-coot-ARG-QVR_link.* . Le fichier acedrg-link-from-coot-ARG-QVR_link-hack.cif est utilisé pour l'affinement dans Phenix en lieu et place du fichier QVR.cif. Attention à vérifier que les atomes d'hydrogène à supprimer dans le fichier PDB après la création de la liaison so…

cryosparc

Anonymous (anonymous@undisclosed.example.com) — 2024-08-07T15:51:44+00:00

using cryoSPARC modify the particles.star file from Warp The particles.star files generated by Warp during the on-the-fly processing link each particle to its tif movie. To import the particles in cryoSPARC and keep the link with the motion corrected micrographs, the star file must be edited.

crystallization

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:50+00:00

Crystallization Cryoprotectants In situ proteolysis Lysine methylation

crystallography

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:42+00:00

Crystallography Data Collection * Prepare loops * In-house * Synchrotron Dataset storage Save the frames from the datasets in \syno\frames\date_beamline. Don't forget to unprotect the folders with chmod -R 777 Data processing Create a directory \syno\frames\proc_date_beamline

dmp

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:50+00:00

CBI Electron Microscopy Platform: Data Management Plan This document describes the constraints imposed by the platform on the different storage locations it makes available to teams and external clients.All storage is organised in teams which are subdivided into projects within datasets are stored.

driver_nvidia

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:52+00:00

Pour la stéréo, il me semble qu’elle n’est plus supportée depuis un moment () Je vais regarder mais j’ai un doute sur le fait qu’elle fonctionne avec la version actuelle du driver. Pour ce qui est du driver nvidia, on le sait, on évite de mettre à jour le driver sur les autres machines : menkab est sous 390.144, et d'après ce que j'ai lu la 419.67 est encore compatible. Peut-être que la version actuelle sur pollux (460.80) ne l'est plu…

elabftw

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:42+00:00

Bonjour Luc, Votre serveur est prêt. La machine s'appelle serv-cavareli1 et elle est accessible en interne uniquement (serv-cavareli1.labo.igbmc.u-strasbg.fr). Ce serveur est une machine virtuelle sous Debian 8. J'ai installé les outils suivants pour vos applications : - nginx - php-fpm - mysql

electron_microscopy

Anonymous (anonymous@undisclosed.example.com) — 2024-03-28T16:10:00+00:00

Electron microscopy Calpendo Booking system Grids preparation Vitrobot procedure Clipping procedure Chameleon procedure ---------- Grids screening and data collection Titan microscope Titan II microscope Acknowledgement Glacios microscope The Glacios microscope interfaces Basic alignment of the microscope Screening at Glacios Setup automated collect at Glacios Recovering Screening data Recovering collected datasets TF20 microscope TF20 microscope interfaces Screening at TF20 …

emready

Anonymous (anonymous@undisclosed.example.com) — 2024-11-26T15:45:46+00:00

How to Run EMReady EMReady - Huang Laboratory Load the program : On your GPU node module load sbgrid/emready Usage: EMReady.sh in_map.mrc out_map.mrc [Options] Required arguments: * in_map.mrc: File name of input EM density map in MRC2014 format. (not the sharp map !)

etbr_waste

Anonymous (anonymous@undisclosed.example.com) — 2023-11-17T16:41:00+00:00

Ethidium bromide (EtBr) waste Liquids containing EtBr must be treated with activated charcoal and then disposed of down the drain. If you use TBE (Tris-Borate-EDTA Buffer, borate is a CMR): * treat it with activated charcoal to eliminate the EtBr,

evocard

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:58+00:00

Small precision to put at the time to make your request of purchase on the intranet concerning the nomenclature it is necessary to put NA.51 and without forgetting the amount of the refill. Reminder about EVOcard EUROFINS : To recharge your account : Make a purchase request on the platform available on the intranet (it will be processed by the purchasing assistant. No request done by email will be processed.

glacios_alignment

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:44+00:00

Basic Microscope Alignment The microscope should be roughly aligned when you arrive. There is no need to do a complete alignment every session, if the microscope behaves strangely, ask for help! You should perform only two or three steps: * Camera gain reference

glacios_collect

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:54+00:00

Setup an automated data collection at Glacios Beam microprobe and nanoprobe calibrations Prepare the Cross Grating grid for calibration * Introduce the Cross Grating Grid in the column. * Go to x34 Imaging status. * Select 2 positions: a carbon square and an empty square.

glacios_interface

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:54+00:00

The Glacios microscope interfaces The microscope console Location: right in front of you on the desk Role: it provides direct control of some of the most important microscope parts: * Magnification * Electron dose: spot size (C1 lens) and beam spread (C2 lens)

glacios_screening

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:52+00:00

The Screening Pipeline 1. Load Grid * Introduce your grids in the cassette * Cassette position 1 is dedicated to the Cross Grating Grid * Grids are loaded with the C-clip toward position 1 ++ * Load the cassette in the NanoCab. Make sure no contaminant (fiber, hair) entered the NanoCab.

h_s

Anonymous (anonymous@undisclosed.example.com) — 2024-04-10T15:30:07+00:00

Liquid chemicals and their waste Lab coat Powder chemicals to discard Ionising radiations Safety rules in the lab Boric acid, borate and TBE buffer Ethidium bromide waste Weighting CMR or T-labelled chemicals

hpc_account

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:46+00:00

Send an email to Michel Ringenbach with the following information: - In order to give you access to the HPC cluster, I need the public ssh key installed on your personal computer (don't send the private key). Here are information to obtain it (in french): - The theme of your research

hpc_created

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:54+00:00

Your public key is in place on hpc-login (cluster front-end). You should be able to log in without a password on hpc-login. Only the passphrase of your local private key at your station will be requested : ssh -Y @hpc-login.u-strasbg.fr For remote connections (outside the Osiris or UHA network), use the Unistra VPN prior to any connection to hpc-login :

hpc_glogin

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:40+00:00

Cher utilisateur de CAIUS (Cluster de cAlcul Intensif à l'Université de Strasbourg), Nous mettons aujourd'hui en service un second serveur de connexion en complément à hpc-login. Son nom : hpc-glogin.u-strasbg.fr Son atout maître : 2 cartes graphiques Nvidia Tesla V100 Sa fonction essentielle : serveur de visualisation pour vos applications graphiques les plus exigeantes (voir

hpc_hardware

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:48+00:00

Au 19/04/2021, les ressources de calcul disponibles pour la communauté sont composées de 2,8 Po de stockage, de 14792 cœurs de calcul, 73 To de mémoire vive, le tout réparti sur 697 nœuds de calcul : * 10 nœuds AMD Epyc Rome Zen2 7002 (2×24

hpc_igbmc

Anonymous (anonymous@undisclosed.example.com) — 2024-11-26T14:17:07+00:00

IGBMC HPC Cluster Storage of scientific data (link to IT page) * space2 storage (link to IT page) * mendel storage (link to IT page) Scientific calculation (link to IT page) * Quick start guide (link to IT page) * Structural biology softwares available on the cluster * AlphaFold 2 * Relion * EMReady OPEN On Demand (CryoSPARC, Rstudio server, JupyterLab)

hpc_meso_module

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:42+00:00

List of selected structural biology software available on the Unistra HPC crystallography ccp4/ccp4-7.0(latest) phenix/phenix-1.17.1 phenix/phenix-1.18rc7 phenix/phenix-1.20.1-4487(latest) microscopy cistem/cistem-1.0.0(latest) cryodrgn/cryodrgn-0.3.4(latest) ctffind/ctffind-4.1.14(latest) relion/relion-1.3 relion/relion-1.3.gnu relion/relion-1.4.gnu relion/relion-2.0 relion/relion-2.0-cuda relion/relion-2.0-omnipath relion/relion-2.0.3 relion/relion-2.0.3-cuda8 re…

hpc_relion

Anonymous (anonymous@undisclosed.example.com) — 2023-11-09T12:54:14+00:00

2023-11-09 Relion-5 is now installed on the Unistra HPC (hpc-login.u-strasbg.fr). To use it simply load the module: module load relion/relion-5.0 The new version of Relion comes with: 1) Blush regularisation: a machine-learning based prior that improves 3D refinement and classification of low SNR data sets

hpc_usage

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:56+00:00

CONNEXION AUX RESSOURCES TERMINAL Nous vous invitons à vous connecter sur hpc-login.u-strasbg.fr par ssh : ssh -Y @hpc-login.u-strasbg.fr : votre login sur le centre de calcul. L’option -Y permet de propager l’affichage graphique si nécessaire.

hpc

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:40+00:00

request a HPC account HPC account created message use the HPC for calculations use relion on the HPC second HPC server HPC hardware Structural biology softwares available on the cluster

in-house

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:46+00:00

CBI in-house X-ray diffraction on Rigaku FR-X Usage (for Pilatus 300K, outdated) Usage for Eiger 4M Frames storage on Synology Maintenance XDS input file Turn ON Turn OFF

intranet

Anonymous (anonymous@undisclosed.example.com) — 2024-02-20T12:48:30+00:00

Accessing IGBMC services from outside Remote desktop Remote desktop page in French on IT Download the configuration file: * for Windows * for MacOS * for Linux On windows * Double click on the configuration file * Type your login in the format and your password On MacOS * Check that Microsoft Remote Desktop is installed (or install it from AppStore)

ionising_radiations

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:46+00:00

The IGBMC is authorised to hold and handle radioactive elements and X-ray generators for research purposes. This authorization has been granted for 5 years in 2020. * Any operator trained in the use of radioelements or X-rays must strictly observe the safety instructions relating to this handling. He/she protects him/herself and others from exposure and prevents the contamination of people and equipment. He/she also manages the radioactive waste produced.

lab_coat

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:44+00:00

It is mandatory to wear a cotton lab coat at you bench, and take it off when going to the atrium, cafeteria, amphitheater, meeting rooms or toilets. Check that your lab coats are 100% cotton. Otherwise, take back inappropriate lab coats to the laundry service (ground floor) asap to exchange for 100% cotton lab coats.

ligand_building_for_refinement_with_phenix

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:52+00:00

1. Ligand Building Ligand is preferentially built with the Maestro software from Schrodinger suite. Avogadro can also be used. If The ligand is a known compound derivative, it is better to download it (mol2 of pdb format) from the pdb / pubchem / zinc databases to prevent construction mistakes.

liquid_waste

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:54+00:00

We remind you that all liquid chemicals (new and/or waste cans) must be kept in a retention tank. Liquid chemical waste must be collected in 5 liter cans (empty 5 liter ethanol cans) by separating them as follows: * Organic acids (e.g. formic, lactic, acetic acid

login_problems

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:48+00:00

Login problems For different reasons sometimes the user is unable to loggin. A few reason and solutions are given below. The first reason is that if your machine supports stereographics display,then you have to select metacity as ubuntu environment. Otherwise the system will refuse the connection (ubuntu bug due to the stereo).

mendel_projects

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:56+00:00

2023-05-17 C’est prêt. Les espaces projets sont exportés en NFS vers tes machines. Il suffit ensuite, sur chaque machine, de faire : sudo mkdir -f /shared/mendel/projects/StardX sudo mount -t nfs mendel.igbmc.u-strasbg.fr:/projects/StardX /shared/mendel/projects/StardX sudo mkdir -f /shared/mendel/projects/InsiPRMTs-PRMT9 sudo mount -t nfs mendel.igbmc.u-strasbg.fr:/projects/InsiPRMTs-PRMT9 /shared/mendel/projects/InsiPRMTs-PRMT9 sudo mkdir -f /shared/mendel/projects/InsiPRMTs-PRMT2 sudo moun…

mise_en_place_de_sssd

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:50+00:00

Bascule de l’authentification sur sssd dixit Guillaume Seith “ça permet d’avoir un cache local des utilisateurs. Comme ça, même si les serveurs d’authentifications ne sont pas joignables ça ne pose pas de problème.” La “home directory

missing_disks_once_the_machine_has_booted

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:42+00:00

Missing disks once the machine has booted Normally all the disks are mounted during boot time. If something goes wrong you can manually mount the disks if nothing else is pausing a problem. The simplest steps are : * turn a terminal by using the key combination

modelangelo

Anonymous (anonymous@undisclosed.example.com) — 2024-03-08T14:41:07+00:00

ModelAngelo is an automatic atomic model building program for cryo-EM maps. with IGBMC HPC * Upload the protein (and DNA/RNA) sequences as separate fasta files, as well as the map. * Check the hand of the map and flip it in ChimeraX (volume flip #1

modelling

Anonymous (anonymous@undisclosed.example.com) — 2024-03-13T09:16:49+00:00

Using ModelAngelo Using AlphaFold2 on IGBMC HPC Using ChimeraX Ligand building for Refinement with Phenix Virtual docking with the Autodock suite

modul_avail

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:40+00:00

List of selected structural biology software available on the IGBMC HPC crystallography albula/3.2.0 adxv/1.9.14 autoproc/20190214 autoproc/20190301 autoproc/20190923 autoproc/20191129 autoproc/20200206 autoproc/20200319 autoproc/20200918 autoproc/20210420 autoproc/20211020 autoproc/2022…

pb_de_x_serveur_sur_estrella

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:46+00:00

Pb de serveur X sur la machine estrella de Nils Le problème : driver nvidia non reconnu et émetteur stéréo état rouge La solution : consultez la page web ci-dessous pour réinitialiser le serveur X Quick and Easy way to fix X11 issues READ THE COMPLETE TUTORIAL BEFORE TRYING.

pc_maintenance

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:52+00:00

Gestion des PC sous Ubuntu/Linux Une nouvelle gestion de l'authentification des utilisateurs avec SSD Sauvegarde d'une configuration système d'une machine Ubuntu Missing disks once the machine has booted Toggling between graphics and terminal mode Login problems Labo7 disk Reservation website Electronic labnote management 3D Vision stereo with Ubuntu 18.04 X server issues on estrella Driver Nvidia pour la stereo setxxx command not working Zones projets on Mendel

poster_printing

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:42+00:00

Dorénavant pour l'impression de vos posters, veuillez contacter: * Philippe VERLEY philippe.verley@igbmc.fr * Stéphane LORENZI: stephane.lorenzi@igbmc.fr

powder_chemicals_discard

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:40+00:00

Solid (and liquid) chemicals are generally deemed expired after 5 years. Do you have expired or useless chemical solids in your fridge, your freezer or your weighing area? Free the space!!! REMINDER: Plastic containers have also a 5-year shelf life. After this time, the manufacturer no longer guarantees the purity of the product (plastic degradation products are released into the contents). You will find the date on the bottom of the jar, the jars without date are more than 10 years old !

prepare_files

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:48+00:00

Prepare files for PDB deposition The final PDB file and the cleaned MTZ file are required. In the PDB files the first lines should be deleted, up to the line written REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP. Only polymer chains should finish with a

purification

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:50+00:00

Purification Flash-freezing of protein samples for long-term storage Limited proteolysis In-house TEV production

referent

Anonymous (anonymous@undisclosed.example.com) — 2024-02-20T09:32:20+00:00

Referent contact premises maintenance (floor cleaning, window cleaning, pest and insect treatment) Ms. Jessica BASS from the technical office. (Administrative Coordinator of Technical Services) * Tel: 3259 * Email: sigwalt@igbmc.fr

relion

Anonymous (anonymous@undisclosed.example.com) — 2024-08-29T07:12:25+00:00

Relion Log in on the igbmc HPC or the team GPU ssh -X login@hpc.igbmc.fr ssh -X login@phantom-node39 #GPU node for lamour-ruff team module load relion/4.0.0 module load ctffind/4.1.13 module load topaz/0.2.5 Executable location: * CTF estimation/CTFFIND-4.1/CTFFIND-4.1 : /shared/software/ctffind/4.1.13/bin/ctffind

safety_lab

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:52+00:00

Main safety rules in the laboratory 10 Obligations * To identify and locate the sites of security and of safety materials (showers, fire extinguishers, eye cleaners, anti-fire blankets, etc.). * To wear a lab coat at you bench, and take it off when going to the atrium, cafeteria, amphitheatre, meeting rooms.

sagsub

Anonymous (anonymous@undisclosed.example.com) — 2024-08-29T06:56:40+00:00

Streptavidin affinity grids (SAG) lattice subtraction Requested files : * * * * Log onto the Lamour GPU node: ssh my_login@hpc.igbmc.fr ssh my_login@phantom-node39 Place the 4 python scripts in a SAGsub3 folder in your hpc home directory (

sauvegarde_d_une_configuration_systeme_d_une_machine_ubuntu

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:48+00:00

Sauvegarde d'une configuration Ubuntu Cette sauvegarde concerne des fichiers qui sont dans le répertoire /etc. La liste des dossiers et fichiers sauvegardés depuis /etc est donné à la fin. Pour sauvegarder une configuration qui a été modifié il suffit de se déplacer dans le répertoire correspondant au nom de la machine sous le dossier

screening_data

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:56+00:00

Grids screened at the Glacios or TF20 microscopes can be recovered on the PC in room E-00xx at the CBI ground floor with an external disk.

service_mission

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:56+00:00

Dear All, Given the situation of the Missions service, the work plan put in place since October 24th will continue as follows: Mission orders (OM) The Missions service will continue to issue them whether they are OM including expenses with GIE funds, GIE OM without expenses, or OM for the supervisory bodies (CNRS, INSERM, UNISTRA). All these OM can only be issued if the traveler has sent to servicemissions@igbmc.fr all the information concerning his/her reservations or travel tickets: exact a…

setxxx_missing

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:44+00:00

Si les commandes setxxx (setcoot, setphenix, setccp4, ...) ne se lancent pas, vérifier que le terminal est bien sous tcsh et pas sous bash.

sidebar

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:44+00:00

BSI Wiki Common services Cloning Purification Biophysical assays Functional assays Crystallization Crystallography Electron Microscopy Modelling PC Maintenance Administrative procedures H&S

smd

Anonymous (anonymous@undisclosed.example.com) — 2023-12-13T10:41:30+00:00

Why, when I receive funding from the University of Strasbourg or Inserm, do I have to follow CNRS purchasing procedures? Because of the single management delegation! What is the single management delegation? The single management delegation, also known as single management mandate, is a management model implemented in our institute since 1st January 2021. With this model, Inserm and the University of Strasbourg entrust CNRS with the management of their funding. In other words,

start

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:42+00:00

Welcome to the BSI Wiki

stereo

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:42+00:00

From CCP4BB Thanks to everyone who gave helpful suggestions; I now have stereo working on Ubuntu 18.04. To help anyone who comes across this in the CCP4 archives in the future, it was necessary to: 1) Install lightdm and set it as the default display manager. Other display managers that don't do compositing may also work.

team_gpu

Anonymous (anonymous@undisclosed.example.com) — 2024-02-09T09:50:04+00:00

Lamour GPU node The GPU server is installed ate IGBMC for the moment Specs : * CPU : 2x Intel Xeon-G 6330 * RAM : 16x 32GB DDR4-2933/3200 RDIMM (512GB total) * GPU : 4x Nvidia A10 (4x 24GB) * HDD : 6x 1.92 To SSD SAS (1 disk for OS, 5 for scratch)

tf20_interface

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:46+00:00

The TF20 microscope interfaces The microscope console Location: right in front of you on the desk Role: It provides direct control of some of the most important microscope parts: * Magnification * Electron dose: spot size (C1 lens) and beam spread (C2 lens)

tf20_screening

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:40+00:00

Make sure Microscope is in good shape (ppt associated) * a.Make sure HT and FEG are on * On TEM User Interface (TUI) * setup tab > High Tension panel High tension button is highlighted yellow * setup tab > FEG Control panel Operate button is highlighted yellow

the_space_labo7_cavarelli

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:54+00:00

Space "/labo7/cavarelli1" Normally the space “/labo7/cavarelli1” is mounted automatically with the “autofs” service at boot time. If this is not the case, two solutions : * maybe the autofs is down. To start the service enter as administrator : service autofs start

titan_to_process

Anonymous (anonymous@undisclosed.example.com) — 2024-07-25T12:08:17+00:00

Pre-processing of dataset from Titan II 1. Recover the dataset from the microscope Log into cbi-gateway-01 to access the microscope and transfer the data to gateway or storage ssh @cbi-gateway-01 ls /mnt/titan2/offloaddata/TemScripting/EF-Falcon/ rsync -avz --progress /mnt/titan2/offloaddata/TemScripting/EF-Falcon/ /mnt/storage/teams///

titan2_ack

Anonymous (anonymous@undisclosed.example.com) — 2024-03-27T15:45:52+00:00

For people using Titan2 electron microscope, please acknowledge in your publications and thesis as : This work used the Integrated Structural Biology platform of the Strasbourg Instruct-ERIC center IGBMC-CBI supported by FRISBI (ANR-10-INBS-0005) and EquipEx+ France cryo-EM (ANR-21-ESRE-0046).

toggling_between_graphics_and_terminal_mode

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:44+00:00

Toggling between graphics and terminal mode The Ubuntu system by default displays the login in graphics mode. But sometimes, as a user you cannot log in. The best way to solve the problem is to enter the terminal mode by entering : CTRL+ALT+F1.

vitrobot

Anonymous (anonymous@undisclosed.example.com) — 2023-11-01T20:18:44+00:00

Vitrobot procedure The VitrobotTM (Vitrification Robot) is a fully PC-controlled device for vitrification (= rapid cooling) of aqueous samples Before starting * fill a dry 5 L tank with liquid nitrogen * label grid boxes with the name of the experiment

weighting-cmr

Anonymous (anonymous@undisclosed.example.com) — 2023-12-13T09:47:06+00:00

Weigthing CMR or T-labelled chemicals All toxic (SGH6 « T, T+ » picto), carcinogenic, mutagenic, reprotoxic or sensitizing (SGH08 « CMR » picto) hazardous chemicals, have to be stored in room 0025 at IGBMC (« petits produits ») and weighed using the secured weighting system (SWS).