If you're calculating a sequence, suppose you calculate it correctly( for example, you know you're gaining +2 points) but can't really evaluate the final material count correctly(can't tell that you're up a rook for some pawns), if the opponent doesn't really have any proper counterplay in that line, would this still be considered improper calculation? Is it better to track material count during the line or at the end of the line?

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Calculating a line means visualizing the positions along the way, and yes, in particular you must be aware of the material count. The reason is simply that it strongly affects the candidate moves (e.g., if you are attacking down material, you watch out for adversary moves forcing queen trade) and also the decision of where to stop calculating the line.

If you "can't tell that you're up a rook for some pawns", then this is not really a calculation: you cannot visualize the final position, what do you actually know about it? What do you mean by having calculated it?

In general, calculating a long chess line correctly is a vastly more difficult task than keeping track of the material along the calculation, which becomes somewhat automatic as you gain experience. If you have trouble with the material count it is unlikely that your calculation will be of any use.

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