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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 12.1
edited by hakanj
on 2020-11-11 16:28
Change comment: There is no comment for this version
To version 4.1
edited by ecrosas
on 2020-08-24 16:48
Change comment: There is no comment for this version

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1 -10. Data processing
1 +10. Data processing and back up
Author
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1 -XWiki.hakanj
1 +XWiki.ecrosas
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1 +Please visit: [[https:~~/~~/photon-science.desy.de/facilities/petra_iii/beamlines/p11_bio_imaging_and_diffraction/user_information/remote_access/index_eng.html>>url:https://photon-science.desy.de/facilities/petra_iii/beamlines/p11_bio_imaging_and_diffraction/user_information/remote_access/index_eng.html||shape="rect"]]
2 +
1 1  \\
2 2  
3 3  **10.1. Automatic data processing**
4 4  
5 -Unless you un-check the option for the specific acquisition run, some basic auto processing will be done for you. For standard rotational data XDSAPP is run, for strategy calculation we use mosflm and spotfinder from the phenix package to process the heat map for the grid scans. The results are compiled into HTML-files to give you a convenient way of checking them. These files live in the processed folders of the corresponding datasets.  A self refreshing index of all results is created in the beamtimes processed folder. During the beamtime you can open it from file::~/~//gpfs/current/processed/index.html in a browser. All HTML-files will be contained in your copy of the data.
7 +Results of the automatic data processing are only available during the beamtime. To see the data presenter, open a Browser (Open Terminal and type:(% style="color: rgb(51,153,102);" %) firefox(%%)) and type(% style="color: rgb(51,153,102);" %) /gpfs/current/processed/index.html.
6 6  
9 +
10 +\\**10.2. Download your data during or after the beamtime**
11 +
12 + Data are available for download via ftp protocol on the [[Gamma portal>>url:https://gamma-portal.desy.de/||shape="rect"]] as it is described in [[here>>doc:ASAP3.The Gamma Portal.WebHome||shape="rect"]].
13 +
7 7  \\
8 8  
9 -**10.3. Manual data processing onsite**
16 +**10.3. Manual data processing during your beamtime**
10 10  
11 11  Open a terminal (see session 3.2) and type ssh haspp11eval01. You need to open one terminal and ssh to haspp11eval01 for every program you want to use.
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17 17  * for CCP4 type in the terminal (% style="color: rgb(0,128,0);" %)ccp4i
18 18  * for phenix type in the terminal (% style="color: rgb(0,128,0);" %)phenix
19 19  
20 -**10.4. Manual data processing after your beamtime or during remote session**
27 +**10.4. Manual data processing after your beamtime**
21 21  
22 22  Manual data processing after the beamtime is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
23 23  
Confluence.Code.ConfluencePageClass[0]
Id
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1 -188798285
1 +175900867
Title
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1 -10. Data processing
1 +10. Data processing and back up
URL
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1 -https://confluence.desy.de/spaces/11/pages/188798285/10. Data processing
1 +https://confluence.desy.de/spaces/11/pages/175900867/10. Data processing and back up