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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 1.1
edited by ecrosas
on 2020-08-24 16:28
Change comment: There is no comment for this version
To version 3.1
edited by ecrosas
on 2020-08-24 16:45
Change comment: There is no comment for this version

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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 -Results of the automatic data processing are available within the remote session.
3 +**10.1. Automatic data processing**
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.(%%)
6 +\\**10.2. Download your data after the beamtime**
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"]].
9 +
10 +**10.3. Manual data processing during your beamtime**
11 +
12 +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.
13 +
14 +To use crystallographic programs:
15 +
16 +* for XDSAPP type in the terminal (% style="color: rgb(0,128,0);" %)xdsapp
17 +* for imosflm type in the terminal (% style="color: rgb(0,128,0);" %)imosflm
18 +* for CCP4 type in the terminal (% style="color: rgb(0,128,0);" %)ccp4i
19 +* for phenix type in the terminal (% style="color: rgb(0,128,0);" %)phenix
20 +
21 +**10. Manual data processing after your beamtime**
22 +
4 4  Manual data processing is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]].
5 -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"]].
24 +
25 +Accessing data
26 +In a terminal window:
27 +ssh (% class="Object" %)[[username@desy-ps-ext.desy.de>>mailto:username@desy-ps-ext.desy.de||shape="rect"]](%%)
28 +ssh username@desy-ps-cpu
29 +Give your password when prompted
30 +Navigate to data by:
31 +cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID
32 +(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)
33 +\\List of software you can use is at:
34 +(% class="Object" %)[[https:~~/~~/confluence.desy.de/display/IS/Photon+Science>>doc:IS.Photon Science.WebHome||shape="rect"]](%%)
35 +\\You can store analysis results in scratch_cc (temporary/testing results) or processed (final results).
36 +\\To use crystallographic programs:
37 +module avail
38 +module load xray     # sets the environment for xds and helper GUIs such as XDSAPP
39 +module load ccp4/6.4
40 +module load phenix 
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1 -175900798
1 +175900828
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1 -https://confluence.desy.de/spaces/11/pages/175900798/10. Data processing and back up
1 +https://confluence.desy.de/spaces/11/pages/175900828/10. Data processing and back up