Reading the instructions that comes with the software will probably help. You can change several inputs to help adjust the predicted velocity to match the measured velocity.
Case capacity
Weighting factor
Powder burning rate factor
Shot start pressure
Ambient temperature
All of these factors can be adjusted and if you read the manual you will find recommendations of what to adjust first.
The temperature adjustment is enabled when you click on the small icon to the right of the Ratio of specific heats.
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After you click the icon a temperature adjustment icon will appear above the Apply&Calc button
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After you click on the Temperature icon this window will appear
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It's entitled Powder Temperature Variation so the software expects you use the powder temperature but in most situations your powder will be the same temperature as the ambient temperature and it's pretty hard to actually measure the temperature of the powder.
There is no information that I've found that defines a limit to the Ba adjustment but I don't like to change my numbers by more than .1, most often I can get good results with far less of a change, more like plus or minus .02.
Before I start changing the Ba value (which can vary from lot to lot of the same powder) I make sure that I use the proper Shot Start Pressure value based on the recommendations that the software displays in a popup if you hold the your cursor over the value for a second or two.
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The Weighting Factor is another value that I change before I start adjusting the Ba value. This represents the amount of powder that follows the base of the bullet. Most ballisticians use .5 (50% of the powder charge) as the standard value. You can change this up or down a couple tenths (.4 to .6). This value is just a guess and it is controlled by the case shape and powder characteristics, I don't know of any standard that specifies what this value should be in relation to the case or powder so it's just a guess.
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When you decide to change the Ba value some people recommend changing the case capacity instead. I wont change the case capacity by more than half a grain if I've measured it.
A lot of these adjustments are going to be based on what input data you feel has a better chance of being correct. For example, if you have to choose whether to change the Ba value or the case capacity I'd base it on whether I know one or the other for a fact. If I've actually measured the case capacity (in accordance with the software manual's instructions) the I'd probably change the Ba value since I couldn't measure it.