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Changes for page 05. Data processing

Last modified by tabermah on 2024-12-11 11:17
From version 15.1
edited by hakanj
on 2020-12-18 14:59
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To version 20.1
edited by hakanj
on 2022-04-08 11:40
Change comment: There is no comment for this version

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8 8  
9 9  **11.2. 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 +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 -Here you can launch crystallographic programs directly //e.g.//:
13 +Use Maxwell-cluster for data processing as described in the next chapter; on-site, you can directly ssh to username@desy-ps-cpu. 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
19 -
20 20  \\
21 21  
22 22  **11.3. Manual data processing after your beamtime or during remote session**
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"]].
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"]].
25 25  
26 26  //Accessing data from outside the DESY network~://
27 -In a terminal window:
22 +
23 +Accessing the Maxwell cluster is easiest with Max-display:  connect to [[https:~~/~~/max-display.desy.de:3443>>url:https://max-display.desy.de:3443||shape="rect"]] via web browser with the credentials of your scientific account.
24 +
25 +Accesss via 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
28 +
30 30  Give your password when prompted
31 31  Navigate to data by:
32 32  cd /asap3/petra3/gpfs/p11/2020/data/beamtimeID
33 33  
34 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.
35 -\\//List of software you can use is at~://
34 +
35 +(% 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
36 +
37 +The partition in the script is defined psx for external users (ps should be used for internal users of Photon Science).
38 +(% style="color: rgb(51,51,51);text-decoration: none;" %)Copy the script to the folder where you run the processing and launch by (%%)
39 +(% style="color: rgb(51,51,51);text-decoration: none;" %)sbatch xds.sh(%%)
40 +(% 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(%%)
41 +(% style="color: rgb(51,51,51);text-decoration: none;" %)The xds-log you get in a file xds-job-~#~##.out
42 +
43 +(% 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/.
44 +
45 +(% 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
46 +sbatch nxds.sh
47 +
48 +//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).//
38 38  \\//To use crystallographic programs~://
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40 40  module load xray     # sets the environment for xds and helper GUIs such as XDSAPP
41 41  module load ccp4/6.4
42 42  module load phenix 
56 +
57 +\\
58 +
59 +\\
Confluence.Code.ConfluencePageClass[0]
Id
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1 -200517675
1 +256500300
URL
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1 -https://confluence.desy.de/spaces/11/pages/200517675/11. Data processing
1 +https://confluence.desy.de/spaces/11/pages/256500300/11. Data processing