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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 10.1
edited by janmeyer
on 2020-11-11 14:28
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.janmeyer
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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, 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 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"]].
9 -
10 10  \\
11 11  
12 12  **10.3. Manual data processing during your beamtime**
13 13  
14 -10. Manual data processing after your beamtime
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.
15 15  
16 -Manual data processing is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
13 +To use crystallographic programs:
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 +
20 +**10.4. Manual data processing after your beamtime**
21 +
22 +Manual data processing after the beamtime is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
23 +
24 +//Accessing data//
25 +In a terminal window:
26 +ssh (% class="Object" %)[[username@desy-ps-ext.desy.de>>mailto:username@desy-ps-ext.desy.de||shape="rect"]](%%)
27 +ssh username@desy-ps-cpu
28 +Give your password when prompted
29 +Navigate to data by:
30 +cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID
31 +(you can only access the data your Door account was related to during the data collections. if you did not participate to the beamtime but are part of the group and would like to access the data, please contact (whom? I'll try to figure this out)
32 +\\//List of software you can use is at~://
33 +(% class="Object" %)[[https:~~/~~/confluence.desy.de/display/IS/Photon+Science>>doc:IS.Photon Science.WebHome||shape="rect"]](%%)
34 +\\//You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).//
35 +\\//To use crystallographic programs~://
36 +module avail
37 +module load xray     # sets the environment for xds and helper GUIs such as XDSAPP
38 +module load ccp4/6.4
39 +module load phenix 
Confluence.Code.ConfluencePageClass[0]
Id
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1 -175900822
1 +183172586
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/183172586/10. Data processing