There is no more pure joy than RailFanning.

Sir,
You are perfectly right that charting is done by System but please note that the System, in the permitted area, is regulated by the charting person (Officer or clerk, what ever he/she may be, referred to as CO here in after).
It is like this:
VIP allotment is done by the system, yet to which PNRs to allot that quota, within a...
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PNR how many passenger/s are to be allotted with berth/s & rest be left-out, which is the berth to be given to whom – all is regulated by the CO.
Though the Coach and Berth numbers are assigned by the system when booking confirmed (excepting 1st Class and 1st AC), one can specify the Coach number he / she prefers (either we have some other passenger in it or for any reason) and the Booking Official (BO) may help you out by regulating the System.
Single Fare Tickets of journey by 2 or more trains (telescopic fares) is in general denied by the BOs (saying it is not permitted or they are actually not aware of) but the system can be regulated for such issuance.
Boarding point is by default the originating station, but the system can be regulated by the BOs and be assigned a subsequent station.
Charting is in fact, very much regulated with the default working of the System and it is not the case that a button is pressed for ‘go for charting’ and the System does it fully at its own.