Hi Henry >From your description, the problem must be in the size of the Jmol object not being properly set, rather than in the molecule being not centered or truncated.
I've had a look at your 1xww_surfaceV1.htm page. I see you are not using frames (as Otis noticed) but you do have some code (which sounds familiar to me) that was used for calculating the Jmol size relative to frames or windows. Yor code is calculating Jmol w and h as the smaller of window dimensions; this is not what you want. The Jmol object set at that, but your text div is positioned at 60% of width, so they overlap and part of the Jmol is hidden. Or (I haven't checked that) you have css rules for the Jmol that conflct with the Info.width value you set by javascript. Also, things can now be done much easily using css. The ideal is to have all sizes in percent, so they will adapt to any screen size. But that requires css rules for the html and body elements too. Please take a look at my template, http://biomodel.uah.es/Jmol/resizable/ and see if it helps you. A final comment: for my pages I gave up trying to keep using frames; I could not manage to make JSmol work across frames. All my tutorials were converted to nonframe pages that hold divs for Jmol and the text.
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