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Not really, for most save anywhere games, if segmented properly there will be zero frames dropped
All games using any kind of Quake engine (and that's a substantial chunk of FPSes) drop frames when you save and load and there's absolutely nothing you can do about it. I don't know whether using demo recording (when available, which it sometimes isn't) and then stitching together the demos lets you get around this or not.
Bioshock also has unavoidable frame dropping.
I don't know about any other save-anywhere games, but even if you're right that the problem only affects a minority there's still the difficult issue of how to deal with that minority.
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The .5s penalty isn't to adjust the time to make it closer to the actual time. It might say that on the site but that is wrong and it has always been wrong.
People said in the rules thread that the penalty was introduced due to the frame dropping problem. This may be true, it may not, I have no idea to be honest, but unless the thread where the penalty was first introduced is still around I doubt there's any way of knowing, and at any rate it doesn't really matter.
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If there's actually frames dropped in between segments, rare, they are calculated and added to the actual run time, like was done for the portal run.
This simply isn't true. I wish it was, and if you were arguing for this (i.e. making the impact of the penalty the same for all games) instead of simply showing another number on the game page, then I would support you. However, the extra frames being added on is only done when more than 0.5s of frames are dropped or possibly when the frames are dropped on an autosave or other non-penalised save (not sure about the last one).
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if you ask most people who have DLed my HL run from here they'll say it is exactly 31 minutes long, even though I give the run's actual time (with frames dropped from segmentation) at the start of the video which is 29:41 (or 30:06 depending on when you think the run is over).
And why do you care which of those numbers people see? Nobody watching a speedrun cares what the actual final time is (unless they're comparing it to other runs, and even then it doesn't matter that much), they care how effectively the runner has optimised that time. And besides, I'd include the tram ride and the G-Man's speech in timing (you have character control from the start of the tram ride to the moment you enter the final portal, and entering the portal is actually significant character control so I don't really even know why that wasn't included) so I make your run almost 35 minutes pre-penalisation anyway.