First you shoot 5 BKT shots and check in the display that you`ve got a decent tonerange througout the picture. If so you go to manual setting and use the same setting there so that the setting doesn`t change during the time lapse, which will result in flickering in the video. You should also switch over to manual focus after the autofocus is finished.
I use the interval timer on my Nikon D300 to automate the shooting. You need to program the interval between each HDR series(I usually go for 5 to 10 sek intervals depending on how fast the clouds are moving). Then you need to decide how many shots you would like to shoot. For 10 sek film in 24 fps you need...you`ve probably guessed it....240 shots!! I normally bracked 5 shots so then it`s 240x5= 1.200 shots. for 10 sek. film.
Before I do all this I have already set the camera to autobracket 5 shots.
Then you just mount your camera on a tripod, press "play" and wait for it to finish.
I use a 8 gig. memorycard. This is not enough if you want to shoot in raw or fine. I choose the highest quality setting that I can to fit the number of shots I`m going to shoot. I don`t need to shoot in fine, because I know that I`m going to use this as a film and Full HD is 1920 x 1080 pixels so the "normal" resolution is plenty.
When I come home I batch edit the HDRs in Photomatix.
I then put all the Detail Enhanced HDRs into Adobe Lightroom where I adjust levels and vibrance (Lightroom is great for editing many files at once). I export the edited files out of Lighroom and doing so changing the resolution to 1080p and changing the names (custom name with number sequence) of the files so that quick time pro will edit them.
Then I go to Quick Time Pro and open the files in a picture sequence and choose 24 fps. After the sequence is made I export the film to my hardrive.
It is possible to batch edit single raw files in Photomatix.
You need to do it in two steps.
First you need to make the .hdr file. You go to "Automate" and "Single File Conversion"
Then you "tick" the "Convert RAW file into .hdr" button. Selct source folder and hit "run"
When it`s finished you go to "Automate" and "Single File Conversion" again, but this time you choose "Tone Map HDR into JPEG using Details Enhancer. remeber to adjust the settings on the Details Enhancer option. Then you select as the source folder the folder which holds the HDRs you made in step one, and hit run.