1. TexRank – SoakDB (practicals)
XChem training – April 2019

2. Directory Structure Details

3. Working directory Visit -1 is the important one!
You will have a proposal number, starting with lb, something like this:
lb13385
And a visit/session number, eg: lb
You will end up with visits/sessions assigned to both:
The lab: labxchem
And beamline: i04-1
Visit -1 will be a labxchem visit, and will be the working directory for the duration of the project
Other beamline visits will be created for data collection
Other lab visits will be created to trigger lab access
Visit -1 is the important one!

4. Linux and windows Windows world: Linux world:
From linux, the location is accessed via:
/dls/labxchem/data/year/visit/processing
You (or your local contact) will create your subfolders in visit-1 by running:
cd /dls/labxchem/data/year/visit/processing
prepareVisit
From windows (lab PCs mainly), you will have access to your visit -1 working directory via:
the Y drive
Y:\data\year\visit\processing
Windows world:
Y:\data\2016\lb \processing
Linux world:
/dls/labxchem/data/2016/lb /processing

5. Working directory structure
Data collection results and pandda analysis
Links to beamline visit directories (obsolete)
The datafile (and backups)
Directory for lab work (soakDB, echo, shifter)
pdb of a good reference model
TeXRank executable and location for crystal image files (obsolete)

6. Lab 36 directory structure:
Crystal target lists output from TeXRank
csv files for echo soaking
csv files for upload to ispyb
csv files for the shifter
soakDB launcher
Jan 2017
XChem intro - SoakDB tutorial

7. XChem BAGs or multiple projects per proposal
When dealing with several targets or variations of the target in the same proposal, please follow those rules:
For eg: in lb visit:
Create subfolder per project/crystal form/construct such as:
/dls/labxchem/data/year/visit/processing/project1/processing
Run prepareVisit in each subfolder to import soakDB in the correct subfolder for each project.
cd /dls/labxchem/data/year/visit/processing/project1/processing
prepareVisit
Use a UNIQUE soakDB per target/crystal form/construct
Use a UNIQUE protein acronym per soakDB
Jan 2017
XChem intro - SoakDB tutorial

8. Useful linux commands Setup useful commands, do this first:
cd /dls/labxchem/data/year/your-proposal-1/processing/
source ./xchempaths
Which will set paths for these commands:
tserver – to launch a windows remote desktop from linux
xce – to launch XchemExplorer
csv2ispyb - to automatically load the data collection information in iSPyB
prepareVisit - to create the subfolders needed for xchem. It needs to be run under the ‘processing’ folder
Cluster commands below
Checking the status of the cluster:
Type: qstat
r means running
S means suspended (cluster is busy – it will run eventually)
Anything with an E (eg Eqw) is an error - bad
Deleting jobs on the cluster
qdel jobID

9. TeXRank

10.      TeXRank Use ‘tserver’ to go on Windows machine
TexRank shortcut on desktop     
 Select plate
 Select (toggle!!) Formulatrix (RC)
 Select 1 Subwell
 Target dispensing location (right click)
 Save list before moving to next plate (ECHO – 1 Target)
Save to here:
Y:\data\year\visit\processing\lab36\crystal-targets
Repeat steps 1, 2, 4, and 5 (yes, step 2 also, bug!!) for another plate
Arrow keys on keyboard to move previous/next
Check the crystal target output csv files X and Y should be within +/ (for swissCI-3drops)

11. soakDB

12.  SoakDB  Click: Load Data File
The red bar at the top means that the datafile and soakDB are not in sync, that the datafile is currently updating, or there is another error.
Do NOT keep working with a red bar! Try the error reset button (to the right).
Datafile activity is indicated in the bottom left corner
Undo/Do button to roll back in case of error    

13. SoakDB      
After loading datafile, the red bar will be gone, lab visit will be identified
 Select a library from the dropdown; compound information will be populated
 Alternatively, for solvent characterisation or custom library, enter manually in green columns

14. SoakDB     
 Alternatively, for solvent characterisation or custom library, enter manually in green columns

15.   SoakDB  Enter the crystallisation drop volume
 Import plates. Select crystal target lists from TeXRank targeting (csv files)

16. SoakDB  
 Click Create Batches. If 1 batch per plate is selected, each crystal plate will be assigned a batch.
Alternatively, uncheck 1 batch per plate, and enter the desired number of crystals/batch
 or manually assign batch numbers

17. SoakDB   
 Enter the library/compound concentration, and the desired final solvent concentration. Click (re)calculate and add to pending
 Alternatively, manually enter desired values in the green columns, and then click (re)calculate and add to pending

18. SoakDB  
 Example for solvent characterisation: Manually entered 6 concentrations of DMSO, in duplicate.

19. SoakDB

20. SoakDB        
 Before files can be exported, beamline (probably visit -2) and crystal details need to be entered (far right of sheet)

21. SoakDB 
 Click Export Pending. This will place csv files for the Echo into the lab36/echo folder.
One csv file is created for each batch

22. Soak Crystals! Lab demo

23. SoakDB 
 After Echo transfer of each batch, click “done”. This will assign a timestamp to batches that have been soaked

24. SoakDB      
 Repeat for cryo, if necessary

25. SoakDB  
Click Export pending to generate csv files for shifter mounting. One csv file per batch is created.
Tick this box if you are going to use the old shifter 

26. Mount Crystals! Lab demo

27. SoakDB 
 Click Load mounting to load results of crystal mounting

28. SoakDB    Click update ISPyB status
 Click Export pending for ISPyB. A single csv file is created for all pending crystals.

29.      Puck management On the “Pucks” tab:
Enter information in green boxes
Click Update/Save Changes. Click on YES for the pop up on overwriting the list
Puck details will be brought in
Manually enter the storage dewar shelf number for each puck in this column
Click Update/Save Changes again