Update instructions to take runs and scans

The instructions to take a miniDAQ run with a given threshold have been added.

I will proceed in the next days to review the rest

docs/operations/taking-data.md

@@ -2,7 +2,7 @@
 
 The scans and the analyses of the scans need to follow a specific naming convention: 
 
-`<sbit-rate-scan|gbt-phase-scan|latency-scan|dac-scan>-<in|out>-[<comment>-]-<data+revision>`
+`<sbit-rate-scan|gbt-phase-scan|latency-scan|dac-scan>-<in|out>-[<comment>-]-<date+revision>`
 
 Meaningfull scans that are supposed to be stored for future reference are to be stored in the path `/gemdata/data/` with the above naming convention.
 
@@ -28,6 +28,18 @@ To analyze an S-bit scan locate first the output in `/gemdata/runs/minidaq/sBitR
 
 At these point analyze the scan using the command `gemos analyze sbit` from the terminal of `gem-locdaq02`: the path of the input file and output directory need to be specified, as well as the options for the plotting and allowed rate for the thresholds settings. 
 
+## Taking a minidaq run with given threshold
+
+To take a threshold scan, first connect to [RCMS](http://cmsrc-gem.cms:20000/rcms/gui/servlet/FMPilotServlet), then create a miniDAQ3 session or attach to a running session.
+
+From the RCMS interface, click on "Initialize" and "Connect". Open the status table by the appropriate button and open the gem calibration interface in the list of running applications. 
+
+Enable the transfer to tier0 in the drop down window below the "DAQ" system column, if the data are intended to be saved to disk. It is the case if the data are to be given to the DPG for analysis.
+
+Select the "Physics" option in the drop down window. The option to use a given threshold for all VFATs instead of the one from the VFAT configuration can be chosen and the threshold can be set. Click on the "Apply settings" button.
+
+Return to the RMCS interface, press on "Configure" and "Start". Once the statistics will be satisfactory, the run should be stopped with the "Stop" button. Then the miniDAQ instance can be destroyed with the "Destroy" button. 
+
 ## Taking a CSC-EMTF-GEM join run on the integration setup in building 904
 
 This paragraph covers the required actions on the GEM side in order to be able to take cosmic data on the GE1/1 integration setup using as triggers the signals from the ME1/1 chamber, available in the setup.
@@ -51,3 +63,4 @@ CMSGEMOS_CONFIG_NAME=b904int-ge11-join-runs CMSGEMOS_PORT=20100 _build/_install/
 ```
 6. The GEM raw data will be stored in the user's temporary folder, `$TMPDIR`, and overwritten at every run.
    Be careful to save the data somewhere if it is important to be kept.
+