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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 16.1
edited by hakanj
on 2021-03-17 07:37
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To version 1.1
edited by ecrosas
on 2020-08-24 16:28
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1 -11. Data processing
1 +10. Data processing and back up
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1 -XWiki.hakanj
1 +XWiki.ecrosas
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1 -\\
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 2  
3 -**11.1. Automatic data processing**
4 -
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.
6 -
7 -\\
8 -
9 -**11.2. Manual data processing onsite**
10 -
11 -Please do not use the control computers of the beamline (haspp11user01-04) nor the haspp11eval01 for data processing (latter is now fully dedicated to autoprocessing.
12 -
13 -Use Maxwell-cluster for data processing as described in the next chapter; on-site, you can directly ssh to username@desy-ps-cpu or use Max-display by connecting to [[https:~~/~~/max-display.desy.de:3443>>url:https://max-display.desy.de:3443||shape="rect"]] via web browser. Access to Maxwell requires a Scientific Account.
14 -
15 -\\
16 -
17 -**11.3. Manual data processing after your beamtime or during remote session**
18 -
19 -Manual data processing after the beamtime or during a remote session is only available for registered [[DESY Scientific Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
20 -
21 -//Accessing data from outside the DESY network~://
22 -In a terminal window:
23 -ssh (% class="Object" %)[[username@desy-ps-ext.desy.de>>mailto:username@desy-ps-ext.desy.de||shape="rect"]](%%)
24 -ssh username@desy-ps-cpu
25 -Give your password when prompted
26 -Navigate to data by:
27 -cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID
28 -
29 -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.
30 -\\//List of software you can use is at~://
31 -(% class="Object" %)[[https:~~/~~/confluence.desy.de/display/IS/Photon+Science>>doc:IS.Photon Science.WebHome||shape="rect"]](%%)
32 -\\//You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).//
33 -\\//To use crystallographic programs~://
34 -module avail
35 -module load xray     # sets the environment for xds and helper GUIs such as XDSAPP
36 -module load ccp4/6.4
37 -module load phenix 
3 +Results of the automatic data processing are available within the remote session.
4 +Manual data processing is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
5 +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"]].
Confluence.Code.ConfluencePageClass[0]
Id
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1 -202398826
1 +175900798
Title
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1 -11. Data processing
1 +10. Data processing and back up
URL
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1 -https://confluence.desy.de/spaces/11/pages/202398826/11. Data processing
1 +https://confluence.desy.de/spaces/11/pages/175900798/10. Data processing and back up