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

@@ -10,15 +10,21 @@ Meaningfull scans that are supposed to be stored for future reference are to be
 
 ### Starting the S-bit rate scan
 
-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.
+To take an S-bit 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".
+
+Consider that usually S-bits scans are taken without HV amplification to investigate the noise level in the detector, so you might need to take action with the DCS on the HV settings.
+
+Open the [xDAQ](http://srv-s2g18-33-01.cms:20100/urn:xdaq-application:service=calibration) calibration suite. In case the calibration suite page was already opened before, reload the page manually.
 
-From the RCMS interface, click on "Connect" and then "Configure".
+From the dropdown menu, select the calibration type "S-bit ARM DAC scan", then  set the number of iterations in the "Iterations" text box to 6 and leave all the other parameters to their default values. Click on "Apply settings".  
 
-Open the [xDAQ](http://srv-s2g18-33-01.cms:20100/urn:xdaq-application:service=calibration) calibration suite. In case the calibration suite page was already opened before you clicked on "Connect" in RCMS, reload the page manually.
+move to the RCMS interface leaving the calibration web page open and  click "Configure". Then in the calibration web page, press "Run".
 
-From the dropdown menu, select the calibration type "S-bit ARM DAC scan", then  set the number of iterations in the "Iterations" text box to 6 and leave all the other parameters to their default values. Click on "Apply settings" and then "Run".
+While the scan is ongoing, from any p5 GEM DAQ machine check that the output files are being written in `/gemdata/runs/minidaq/sBitRateScan`. You can also check in the logs present in `/gemdata/log/` what the software is doing.
 
-While the scan is ongoing, from any p5 GEM DAQ machine check that the output files are being written in `/gemdata/runs/minidaq/sBitRateScan`.
+The output files needs to be moved otherwise they will get overwritten by the next scan. 
 
 ### Analyzing the S-bit scan