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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 21.1
edited by tabermah
on 2022-05-25 15:29
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To version 2.1
edited by ecrosas
on 2020-08-24 16:36
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1 -11. Data processing
1 +10. Data processing and back up
Author
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1 -XWiki.tabermah
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**
3 +**10.1. Automatic data processing**
4 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.
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**
6 6  
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"]].
8 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. Access to Maxwell requires a Scientific Account.
14 -
15 15  \\
16 16  
17 -**11.3. Manual data processing after your beamtime or during remote session**
12 +**10.3. Manual data processing during your beamtime**
18 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"]].
14 +10. Manual data processing after your beamtime
20 20  
21 -//Accessing data from outside the DESY network~://
22 -
23 -Accessing the Maxwell cluster is easiest with Max-display:  connect to [[https:~~/~~/max-display.desy.de:3443>>url:https://max-display.desy.de:3443||shape="rect"]] via web browser with the credentials of your scientific account.
24 -
25 -Accesss via 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 -
29 -Give your password when prompted
30 -Navigate to data by:
31 -cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID
32 -
33 -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.
34 -
35 -(% 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
36 -
37 -The partition in the script is defined psx for external users (ps should be used for internal users of Photon Science).
38 -(% style="color: rgb(51,51,51);text-decoration: none;" %)Copy the script to the folder where you run the processing and launch by (%%)
39 -(% style="color: rgb(51,51,51);text-decoration: none;" %)sbatch xds.sh(%%)
40 -(% 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(%%)
41 -(% style="color: rgb(51,51,51);text-decoration: none;" %)The xds-log you get in a file xds-job-~#~##.out
42 -
43 -(% style="color: rgb(51,51,51);text-decoration: none;" %)nxds can be used for processing Serial Crystallography data in a similar way than xds. As the computing time is long, nxds should should be used via a script to queue the jobs in slurm. The template script (nxds.sh) as well as an example of input file (nXDS.INP) can be found in /asap3/gpfs/common/p11/.
44 -
45 -(% style="color: rgb(51,51,51);text-decoration: none;" %)Copy the script and the nXDS.INP to the folder where you run the processing. The nXDS.INP file needs some editing to fit your data path and data collection parameters (wavelength, detector distance, oscillation...). The processing is launch by
46 -sbatch nxds.sh
47 -
48 -//List of software you can use is at~://
49 -(% class="Object" %)[[https:~~/~~/confluence.desy.de/display/MXW/Photon+Science>>doc:MXW.Photon Science.WebHome||shape="rect"]](%%)
50 -\\//You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).//
51 -\\//To use crystallographic programs~://
52 -module avail
53 -module load xray     # sets the environment for xds and helper GUIs such as XDSAPP
54 -module load ccp4/6.4
55 -module load phenix 
56 -
57 -\\
58 -
59 -\\
60 -
61 -(% style="left: 50.0%;top: 50.0px;" %)
62 -(((
63 -\\
64 -)))
16 +Manual data processing is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
Confluence.Code.ConfluencePageClass[0]
Id
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1 -275744716
1 +175900822
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/275744716/11. Data processing
1 +https://confluence.desy.de/spaces/11/pages/175900822/10. Data processing and back up