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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 33.1
edited by tabermah
on 2024-09-23 16:39
Change comment: There is no comment for this version
To version 37.1
edited by tabermah
on 2024-09-24 11:14
Change comment: There is no comment for this version

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80 80  (% style="text-align: justify;" %)
81 81  The processing folders contain two folders, 'xdsapp' and 'manual'. 'Manual' contains a template for manual processing having all the correct parameters. However, to shorten the processing time and make use of the computational structure, reprocessing your data on the maxwell nodes should be done by using a script to queue the jobs in slurm:
82 82  
83 -* a template scripts can be found at /asap3/petra3/gpfs/common/p11/processing_scripts/
84 -** (% style="color: rgb(0,0,0);text-decoration: none;" %)xds_users.sh For (% style="color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)external (% style="color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0); color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)a(% style="color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0); color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0); color: rgb(255, 0, 0)" %)cademic (% style="color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)users
85 -** xds_inhouse.sh For (% style="color: rgb(255,0,0);" %)in-house users
86 -* (% style="color: rgb(0,0,0);" %)differences on the scripts are on the partition used for the processing (i.e. //pscpu// should be used for internal users of Photon Science and //psxcpu// for external academic users)
83 +* template scripts can be found at /asap3/petra3/gpfs/common/p11/processing_scripts/
84 +** (% style="color: rgb(0,0,0);text-decoration: none;" %)xds_users.sh For (% style="color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)external users
85 +** xds_inhouse.sh For (% style="color: rgb(255,0,0);" %)in-house users
86 +* (% style="color: rgb(0,0,0);" %)differences on the scripts are on the partition (i.e. //pscpu// should be used for internal users of Photon Science and //psxcpu// for external users) and the xds version used for processing
87 87  * (% style="color: rgb(0,0,0);" %)copy the script to the folder where you run the processing
88 -* (% style="color: rgb(0,0,0);" %)launch the script by typing sbatch xds(% style="color: rgb(0, 0, 0); color: rgb(255, 0, 0)" %)_(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)name_of_the_script(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); text-decoration: none" %).sh (e.g., //sbatch xds_users.sh //for external users )
88 +* (% style="color: rgb(0,0,0);" %)launch the script by typing //sbatch xds//(% style="color: rgb(0, 0, 0); color: rgb(255, 0, 0)" %)//_//(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); text-decoration: none; color: rgb(255, 0, 0)" %)//name_of_the_script//(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); text-decoration: none" %)//.sh// (e.g., //sbatch xds_users.sh //for external users )
89 89  * (% style="color: rgb(0,0,0);" %)the script will find a free node for your job to run fast
90 90  * (% style="color: rgb(0,0,0);" %)the xds-log you get in a file xds-job-~#~##.out.
91 91  
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121 121  To use crystallographic programs type in terminal (for example):
122 122  
123 123  * **module avail** #to check what programs and versions are available
124 -* **module load xray** # sets the environment for xds and helper GUIs such as (% style="color: rgb(0,0,0);" %)XDSAPP
124 +* **module load xray** # sets the environment for old xds and helper GUIs such as (% style="color: rgb(0,0,0);" %)XDSAPP
125 +* (% style="color: rgb(0,0,0);" %)**module load maxwell xds** # sets the environment for new xds
125 125  * **module load ccp4/7** # sets the environment for ccp4 version 7
126 126  * **module load phenix** # sets the environment for phenix
127 127  
Confluence.Code.ConfluencePageClass[0]
Id
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1 -379128863
1 +175900747
URL
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1 -https://confluence.desy.de/spaces/11/pages/379128863/11. Data processing
1 +https://confluence.desy.de/spaces/11/pages/175900747/11. Data processing