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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 7.1
edited by ecrosas
on 2020-09-09 16:46
Change comment: There is no comment for this version
To version 17.1
edited by hakanj
on 2021-04-12 20:51
Change comment: There is no comment for this version

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1 -XWiki.ecrosas
1 +XWiki.hakanj
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1 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:(% style="color: rgb(51,153,102);" %) firefox(%%)) and type(% style="color: rgb(51,153,102);" %) /gpfs/current/processed/index.html.
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 6  
7 -
8 -\\**10.2. Download your data during or after the beamtime**
9 -
10 - Data are available for download via ftp protocol on 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"]].
11 -
12 12  \\
13 13  
14 -**10.3. Manual data processing during your beamtime**
9 +**11.2. Manual data processing onsite**
15 15  
16 -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.
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.
17 17  
18 -To use crystallographic programs:
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.
19 19  
20 -* for XDSAPP type in the terminal (% style="color: rgb(0,128,0);" %)xdsapp
21 -* for imosflm type in the terminal (% style="color: rgb(0,128,0);" %)imosflm
22 -* for CCP4 type in the terminal (% style="color: rgb(0,128,0);" %)ccp4i
23 -* for phenix type in the terminal (% style="color: rgb(0,128,0);" %)phenix
15 +\\
24 24  
25 -**10.4. Manual data processing after your beamtime**
17 +**11.3. Manual data processing after your beamtime or during remote session**
26 26  
27 -Manual data processing after the beamtime is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
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"]].
28 28  
29 -//Accessing data//
21 +//Accessing data from outside the DESY network~://
30 30  In a terminal window:
31 31  ssh (% class="Object" %)[[username@desy-ps-ext.desy.de>>mailto:username@desy-ps-ext.desy.de||shape="rect"]](%%)
32 32  ssh username@desy-ps-cpu
33 33  Give your password when prompted
34 34  Navigate to data by:
35 -cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID
36 -(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)
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(%%)
37 37  \\//List of software you can use is at~://
38 38  (% class="Object" %)[[https:~~/~~/confluence.desy.de/display/IS/Photon+Science>>doc:IS.Photon Science.WebHome||shape="rect"]](%%)
39 39  \\//You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).//
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1 -183171859
1 +202398829
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1 -https://confluence.desy.de/spaces/11/pages/183171859/11. Data processing
1 +https://confluence.desy.de/spaces/11/pages/202398829/11. Data processing