Wiki source code of 10. Data processing and back up
Version 3.1 by ecrosas on 2020-08-24 16:45
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1.1 | 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"]] |
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2.1 | 3 | **10.1. Automatic data processing** |
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3.1 | 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.(%%) |
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2.1 | 6 | \\**10.2. Download your data after the beamtime** |
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| 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"]]. | ||
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| 10 | **10.3. Manual data processing during your beamtime** | ||
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3.1 | 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. |
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3.1 | 14 | To use crystallographic programs: |
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| 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 | ||
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| 21 | **10. Manual data processing after your beamtime** | ||
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1.1 | 23 | Manual data processing is only available for registered [[DESY Science Accounts>>doc:FSEC.Science Accounts.WebHome||shape="rect"]]. |
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3.1 | 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 |