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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 2.1
edited by ecrosas
on 2020-08-24 16:36
Change comment: There is no comment for this version
To version 13.1
edited by hakanj
on 2020-12-18 14:57
Change comment: There is no comment for this version

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1 -10. Data processing and back up
1 +10. Data processing
Author
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1 -XWiki.ecrosas
1 +XWiki.hakanj
Content
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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"]]
1 +\\
2 2  
3 3  **10.1. Automatic data processing**
4 4  
5 -Results of the automatic data processing are only available during the beamtime. To see the data presenter, open a Browser (Open Terminal and type: firefox) and type /gpfs/current/processed/index.html.
6 -\\**10.2. Download your data after the beamtime**
5 +Unless you un-check the option for the specific acquisition run, autoprocessing will be executed. For standard rotational data autoprocessing is via XDSAPP (Sparta et al. (2016) //J. Apple. Cryst.// **49**, 1085-1092) for strategy calculation we use Mosflm (Leslie //Acta D//**62** (2006) 48-57) and Spotfinder ((% style="color: rgb(0,0,0);text-decoration: none;" %)Zhang et al. (2006). (% style="text-decoration: none;text-align: left;" %)//J. Appl. Cryst.//(% style="color: rgb(0,0,0);text-decoration: none;" %) (% style="text-decoration: none;text-align: left;" %)**39**(% style="color: rgb(0,0,0);text-decoration: none;" %), 112–119)(%%) for producing the heatmap for the grid scans. The results are compiled into HTML-files to give you a convenient way of checking them. The output files are 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. The HTML-file is also contained in your data backup.
7 7  
8 - Data are available for download via 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"]].
7 +\\
9 9  
9 +**10.3. Manual data processing onsite**
10 +
11 +Open a terminal (see session 3.2) and type ssh haspp11eval01. Please do not use the control computers of the beamline (haspp11user01-04) for data processing.
12 +
13 +Here you can launch crystallographic programs directly //e.g.//:
14 +
15 +* for XDSAPP type in the terminal (% style="color: rgb(0,128,0);" %)xdsapp
16 +* for imosflm type in the terminal (% style="color: rgb(0,128,0);" %)imosflm
17 +* for CCP4 type in the terminal (% style="color: rgb(0,128,0);" %)ccp4i
18 +* for phenix type in the terminal (% style="color: rgb(0,128,0);" %)phenix
19 +
10 10  \\
11 11  
12 -**10.3. Manual data processing during your beamtime**
22 +**10.4. Manual data processing after your beamtime or during remote session**
13 13  
14 -10. Manual data processing after your beamtime
24 +Manual data processing after the beamtime or during a remote session is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
15 15  
16 -Manual data processing is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
26 +//Accessing data from outside the DESY network~://
27 +In a terminal window:
28 +ssh (% class="Object" %)[[username@desy-ps-ext.desy.de>>mailto:username@desy-ps-ext.desy.de||shape="rect"]](%%)
29 +ssh username@desy-ps-cpu
30 +Give your password when prompted
31 +Navigate to data by:
32 +cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID
33 +
34 +Data is accessible to users who were registered participants to the experiment in Door prior to the beamtime ID being opened at the beamline. If you cannot access the data, please contact your LC or the beamline manager.
35 +\\//List of software you can use is at~://
36 +(% class="Object" %)[[https:~~/~~/confluence.desy.de/display/IS/Photon+Science>>doc:IS.Photon Science.WebHome||shape="rect"]](%%)
37 +\\//You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).//
38 +\\//To use crystallographic programs~://
39 +module avail
40 +module load xray     # sets the environment for xds and helper GUIs such as XDSAPP
41 +module load ccp4/6.4
42 +module load phenix 
Confluence.Code.ConfluencePageClass[0]
Id
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1 -175900822
1 +188798286
Title
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1 -10. Data processing and back up
1 +10. Data processing
URL
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1 -https://confluence.desy.de/spaces/11/pages/175900822/10. Data processing and back up
1 +https://confluence.desy.de/spaces/11/pages/188798286/10. Data processing