https://bsi.inscog.eu/ 2026-06-01T21:59:08+00:00 https://bsi.inscog.eu/ https://bsi.inscog.eu/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2023-11-01T20:19:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=crystallography:processing:aimless_procedure&rev=1698869950&do=diff Aimless >setccp4 >ccp4i Create a project in the /ccp4 subfolder Run Aimless * If XDS was used before, choose the to prevent scaling a second time * If there are several datasets/scans for the same crystal scale and merge all sets in Aimless text/html 2023-11-01T20:19:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=crystallography:processing:cif&rev=1698869948&do=diff Generate PDB and CIF restrain files for ligands of the LH series * Prepare the 2D chemical structure using Marvin Sketch (ChemAxon) * Add hydrogen atoms to the structure (Structure>Add>Explicit hydrogens) * Convert to 3D (Structure>Clean 3D>Clean in 3D) text/html 2023-11-01T20:19:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=crystallography:processing:igbmc_cluster&rev=1698869950&do=diff Access and usage of the IGBMC HPC cluster First you need to verify that your environment is properly set. >ssh login@surf The sbatch command allow you to submit a script with commands to the cluster >sbatch -p surf cmd * The command then gives a job execution number. text/html 2023-11-01T20:19:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=crystallography:processing:microscopy_cluster&rev=1698869950&do=diff Access and usage of the CBI Microscopy calculation cluster Access to the machine compute1 >ssh login@img-compute1 The softwares are on /usr/local and the script corresponding to each program has to be run (similar to what is done by the setxxx commands). text/html 2023-11-01T20:19:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=crystallography:processing:resolution_cut&rev=1698869948&do=diff What is the resolution limit to choose ? As recommended by Diederich, keep everything up to CC(1/2) of 0.1 in XDS A CC* of 0.5 corresponds to CC(1/2) of 0.15 Paired refinement: to get the statistics of a modeled refined at “high resolution” to a given text/html 2023-11-01T20:19:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=crystallography:processing:structure_polishing&rev=1698869948&do=diff Structure polishing For the validation of datasets and models, use the “paired refinement” procedure (evolution and comparisonof CC*, CCWORK and CCFREE). For a structure in an advanced state, always compare our results (datasets/models) with the automated protocols PDB_REDO and Phenix Optimize final model [alpha]. For confidentiality issues PDB_REDO will be instaled locally. text/html 2023-11-01T20:19:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=crystallography:processing:xds_detailed_procedure&rev=1698869950&do=diff How to obtain the best data from XDS The procedures for processing data with XDS have been described [4, 5] and are not repeated here. Instead, based on first hand experiences when processing datasets from my own group and helping others with their challenging datasets, I focus on those steps that are critical for data quality. For simplicity, we assume that a given dataset can be indexed in the correct space group. The overarching rules for data processing, in the order of their importance, ar… text/html 2023-11-01T20:19:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://bsi.inscog.eu/doku.php?id=crystallography:processing:xds_procedure&rev=1698869948&do=diff XDS procedure >setxds >xdsgui Create a project in the xds subfolder Load the first frame of the dataset from /syno/frames/date_beamline/drop/... Generate XDS.INP Run XDS * if the correct spacegroup and cell parameters were not identified by IDREF, provide them in XDS.INP