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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 13.1
edited by hakanj
on 2020-12-18 14:57
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To version 11.1
edited by hakanj
on 2020-11-11 16:28
Change comment: There is no comment for this version

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2 2  
3 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 +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.
6 6  
7 7  \\
8 8  
9 9  **10.3. Manual data processing onsite**
10 10  
11 -Open a terminal (see session 3.2) and type ssh haspp11eval01. Please do not use the control computers of the beamline (haspp11user01-04) for data processing.
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.
12 12  
13 -Here you can launch crystallographic programs directly //e.g.//:
13 +To use crystallographic programs:
14 14  
15 15  * for XDSAPP type in the terminal (% style="color: rgb(0,128,0);" %)xdsapp
16 16  * for imosflm type in the terminal (% style="color: rgb(0,128,0);" %)imosflm
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17 17  * for CCP4 type in the terminal (% style="color: rgb(0,128,0);" %)ccp4i
18 18  * for phenix type in the terminal (% style="color: rgb(0,128,0);" %)phenix
19 19  
20 -\\
20 +**10.4. Manual data processing after your beamtime**
21 21  
22 -**10.4. Manual data processing after your beamtime or during remote session**
22 +Manual data processing after the beamtime is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
23 23  
24 -Manual data processing after the beamtime or during a remote session is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
25 -
26 -//Accessing data from outside the DESY network~://
24 +//Accessing data//
27 27  In a terminal window:
28 28  ssh (% class="Object" %)[[username@desy-ps-ext.desy.de>>mailto:username@desy-ps-ext.desy.de||shape="rect"]](%%)
29 29  ssh username@desy-ps-cpu
30 30  Give your password when prompted
31 31  Navigate to data by:
32 -cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID
33 -
34 -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 +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)
35 35  \\//List of software you can use is at~://
36 36  (% class="Object" %)[[https:~~/~~/confluence.desy.de/display/IS/Photon+Science>>doc:IS.Photon Science.WebHome||shape="rect"]](%%)
37 37  \\//You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).//
Confluence.Code.ConfluencePageClass[0]
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1 -188798286
1 +183172589
URL
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1 -https://confluence.desy.de/spaces/11/pages/188798286/10. Data processing
1 +https://confluence.desy.de/spaces/11/pages/183172589/10. Data processing