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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
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To version 17.1
edited by hakanj
on 2021-04-12 20:51
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1 -10. Data processing and back up
1 +11. Data processing
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1 -XWiki.ecrosas
1 +XWiki.hakanj
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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 -**10.1. Automatic data processing**
3 +**11.1. 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 +**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 +
10 10  \\
11 11  
12 -**10.3. Manual data processing during your beamtime**
17 +**11.3. Manual data processing after your beamtime or during remote session**
13 13  
14 -10. Manual data processing after your beamtime
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"]].
15 15  
16 -Manual data processing is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
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 +
31 +(% style="color: rgb(51,51,51);text-decoration: none;" %)Our processing folders now contain two folders, 'full' and 'manual'. 'Manual' contains a template that has all the correct parameters and processing will run just by typing xds_par there. However, to shorten the processing time and make use of the computational structure, you should use a script to queue the jobs in slurm. A template script (xds.sh) can be found at /asap3/petra3/gpfs/common/p11/xds.sh(%%)
32 +(% style="color: rgb(51,51,51);text-decoration: none;" %)Copy the script to the folder where you run the processing and launch by (%%)
33 +(% style="color: rgb(51,51,51);text-decoration: none;" %)sbatch xds.sh(%%)
34 +(% style="color: rgb(51,51,51);text-decoration: none;" %)It will find a free node for your job and run faster than just typing xds_par(%%)
35 +(% style="color: rgb(51,51,51);text-decoration: none;" %)The xds-log you get in a file xds-job-~#~##.out(%%)
36 +\\//List of software you can use is at~://
37 +(% class="Object" %)[[https:~~/~~/confluence.desy.de/display/IS/Photon+Science>>doc:IS.Photon Science.WebHome||shape="rect"]](%%)
38 +\\//You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).//
39 +\\//To use crystallographic programs~://
40 +module avail
41 +module load xray     # sets the environment for xds and helper GUIs such as XDSAPP
42 +module load ccp4/6.4
43 +module load phenix 
Confluence.Code.ConfluencePageClass[0]
Id
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1 -175900822
1 +202398829
Title
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1 -10. Data processing and back up
1 +11. 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/202398829/11. Data processing