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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 11.1
edited by hakanj
on 2020-11-11 16:28
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To version 19.1
edited by pompidor
on 2021-12-03 11:12
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1 -10. Data processing
1 +11. Data processing
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1 -XWiki.hakanj
1 +XWiki.pompidor
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1 1  \\
2 2  
3 -**10.1. Automatic data processing**
3 +**11.1. Automatic data processing**
4 4  
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.
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 7  \\
8 8  
9 -**10.3. Manual data processing onsite**
9 +**11.2. Manual data processing onsite**
10 10  
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.
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 12  
13 -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.
14 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
15 +\\
19 19  
20 -**10.4. Manual data processing after your beamtime**
17 +**11.3. Manual data processing after your beamtime or during remote session**
21 21  
22 -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"]].
23 23  
24 -//Accessing data//
21 +//Accessing data from outside the DESY network~://
25 25  In a terminal window:
26 26  ssh (% class="Object" %)[[username@desy-ps-ext.desy.de>>mailto:username@desy-ps-ext.desy.de||shape="rect"]](%%)
27 27  ssh username@desy-ps-cpu
28 28  Give your password when prompted
29 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~://
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 +
33 +The partition in the script is defined psx for external users (ps should be used for internal users of Photon Science).
34 +(% style="color: rgb(51,51,51);text-decoration: none;" %)Copy the script to the folder where you run the processing and launch by (%%)
35 +(% style="color: rgb(51,51,51);text-decoration: none;" %)sbatch xds.sh(%%)
36 +(% 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(%%)
37 +(% style="color: rgb(51,51,51);text-decoration: none;" %)The xds-log you get in a file xds-job-~#~##.out
38 +
39 +(% 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/.
40 +
41 +(% 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
42 +sbatch nxds.sh
43 +
44 +//List of software you can use is at~://
33 33  (% class="Object" %)[[https:~~/~~/confluence.desy.de/display/IS/Photon+Science>>doc:IS.Photon Science.WebHome||shape="rect"]](%%)
34 34  \\//You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).//
35 35  \\//To use crystallographic programs~://
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37 37  module load xray     # sets the environment for xds and helper GUIs such as XDSAPP
38 38  module load ccp4/6.4
39 39  module load phenix 
52 +
53 +\\
54 +
55 +\\
Confluence.Code.ConfluencePageClass[0]
Id
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1 -183172589
1 +252809700
Title
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1 -10. Data processing
1 +11. Data processing
URL
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1 -https://confluence.desy.de/spaces/11/pages/183172589/10. Data processing
1 +https://confluence.desy.de/spaces/11/pages/252809700/11. Data processing