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For brightly lit scenes with foreground and background (sky with clouds) elements, meter to capture foreground shadow detail and apply an ND grad filter (I typically use a 2-stop soft) to the sky. Otherwise it is impossible to avoid blowing out at least part of the sky detail.
Many of St. Ansel's most spectacular landscape/cloud photographs (Clearing Winter Storm, etc.) were shot in low contrast situations where the film was better able to retain both shadow and cloud detail.
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If you insist on using the zone system, meter the whitest part of the cloud, set that as white with no detail, and develop appropiately. You will most likely find yourself doing N-1 or N-2 so remember to increase exposure.
Good luck.
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The zone system will keep you from blowing out the highlights, and losing detail in the shadows, that is it will put the scene values inside the film's range or warn you if the scene's range exceeds the film's. Clouds can be made more dramatic with yellow, or even more with red filters (for b/w only!).
A polarizing filter can be used for color too, but it doesn't work in all cases. Works best if you are aiming about at right angles to the sun. So it doesn't help sunsets or sunrises very much.
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Another thought is to develop in PYRO, or other compensating developer.
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It partly depends on the tone of the clouds. If you're talking about a white/very bright gray fluffy type cloud in a blue sky the bright white areas of the cloud are usually the brightest areas in the scene so I typically place them on Zone VII. If that results in the shadows being too dark (e.g. Zone II or lower, maybe Zone III or lower since I usually place the darkest important shadow on Zone IV rather than III) I meter and expose for the darkest important shadow area and then plan on minus development (with black and white photography) to bring the brightest part of the clouds down to Zone VII or so. If you're talking about dramatic dark gray clouds as in a gathering storm then I just meter the brightest area and place it where I want it, usually Zone V or VI, assuming that doesn't mess up something else in the scene. Sometimes just using a polarizer will help. The polarizer will darken a blue sky to some extent depending on the angle of the light source and darkening the blue sky surrounding the clouds will make the clouds look brighter without actually doing anything to the clouds themselves.
When you say the clouds come out "weak" what do you mean - not bright enough or so bright that all texture is lost and they just look like white blobs? The cure is different depending on which you mean. If you mean they're white blobs because placing the darkest important shadow on Zone III or higher moved the cloud up to Zone VIII or higher then with b&w photography the cure is minus development. If you mean they aren't bright enough then the cure is plus development. I guess the same is true to some extent with color photography since color film (at least color negative film) can be pushed or pulled but I don't do enough color photography to really know how much latitude you have for plus and minus development with it.
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Since James' clouds come out "weak" when he meters for his foreground shadow areas, I assumed that his sky area is getting overexposed, resulting in a loss of cloud contrast and detail. James, if this is not the case, please enlighten us!
In the southwestern U.S. where I live, grand landscapes benefit greatly from cross-lit texture, which is minimized by N- development. That is why I prefer to use an ND grad filter where possible to hold back the sky, with N- development as a fallback.
Brian, color film is better at being pushed than pulled. For example, Provia 100F can be pushed up to 2 stops and pulled up to 0.5 stops, according to Fuji. I am not familiar with color negative films being pushed and pulled. The color neg films I use (Fuji 160S and Kodak 160VC) do not have push/pull specs from their manufacturers, presumably because with such wide exposure latitude it was deemed unnecessary (or perhaps it just doesn't work with these films).
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Basically, what Brian Ellis said. Place the shadows you want to hold detail on Zone III. This sets your exposure. Then find the value of the brightest clouds that you want to hold detail. Adjust development so that this falls on Zone VII. It really is just that simple in concept. Of course it's a bit more complicated in practice, because you have to have already nailed your EI and your N, N+ and N- developement times. With them, the Zone System can be a precision tool. Without them, the Zone System becomes just another way to guess.
I disagree with Jim Galvin a bit. My interpretation of the Zone System isn't quite the same. Jim implies that the purpose is to keep the scene's range from exceeding the film's range. I think the purpose is to fit the scene's range into the paper's range.
A blown out highlight is not a film phenomenon. It's a photo paper phenomenon. The dynamic range of film far exceeds the dynamic range of photo paper. The Zone System is designed to use the film as an intermediary to shoe-horn the subject brightness range (SBR) into the available photo paper density range, thus avoiding blown out highlights. It's a different way of looking at it. Make of it what you will.
On the topic of filters, note that yellow, orange, and red filters have little effect on the clouds. They effect the blue sky around the clouds. Basically, the filters increase (a little or a lot, depending on the filter) the range between the clouds and the blue sky. Another way to look at it is the filters darken the blue sky while leaving the clouds pretty much alone. If the sky is nothing but white and grays, filters will be of little help.
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As Bruce has pointed out, the whiteness of the clouds cannot be reduced, but we can "sculpt" around them with filters. If the clouds contain shadowy areas, they can be rendered more 3-dimensional, by lowering the values around and between them.
Polarizing filters can work wonders, especially when shooting at a right-angle to the sun. Since they can be rotated, one can adjust them to suit one's taste. Unlike Yellow/Orange/Red filters, they have little effect on natural colors, such as green leaves, and remove much of the need for a graduated filter (or gradient layer in Photoshop).
In black and white, you can combine a polarizer with a medium yellow filter and get the results of a deep Orange filter, without rendeering foliage as charcoal. You can control the amount of haze that you want to see, which indicates distance.
Of course the best thing is to move back in time a few hundred years, before the Industrial Revolution. The skies were much cleaner then.
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I only shoot black and white film and I am rather new to the zone system, but I still get confused with the n + or - part of it. If I put my shadow in Zone III and then measure the highlight of the clouds, the big puffy white ones , and they regester 5 or more stops from shadow III then I should which, incease or decrease my developement time. My skys and clouds tend to come out without alot of defination in the neg. and most of the time its hard to tell them apart. So when I print the neg. I spend alot of time trying to burn the clouds in. If I am getting the shadow where I want it, then It has to be a development problem, right? If it is a low contrast exposure, I need to develop the film longer, and if it is a high contrast exposure I would need to develope less, Right or wrong? Thanks for all of your patience , James