Miguel, I do apologize for taking so much of your time before getting at these points. I probably did misunderstand you in a few ways. The problem is that I'm doing all this on the side while doing a completely unrelated job in the IT industry (or Xmas preparations this week) and haven't had the time to really look at the applet. Besides, I was waiting for version 10. That is the version I am so very impressed with.
You said in the first line of your previous email:
If you are writing a standalone java application then you do not want to use the JmolApplet.
I must admit I didn't check examples/Integration.java as I don't currently have a Jmol version on disk, and I'm on a slow phone line. I just assumed from previous knowledge that your first line meant I was to look at the application rather than the applet. If you meant some component inside the applet it indeed seems perfect. Maybe for some kind of compatability with my previous code I'd still take the applet object itself, but I'll look into that. Browsing the CVS to look at Integration.java I see that I may have looked at it earlier, but didn't understand the relation of JmolViewer to the applet or application. I think I have enough information now and will give this a try some time in January.
This feeling of not being heard came because I don't remember having a direct answer to my issues as you have given now. I am very grateful, and pleased with the answers. Now here are some further responses.
Atom positions have *never* been moved. If bonds are specified then they are applied, regardless of distance/length.
Okay. I didn't expect Jmol to move atom positions, but wanted to make sure. This had certainly not been answered before. In terms of bonds, I read the responses and related discussions carefully and didn't achieve complete certainty about this point. "If bonds are specified then they are applied" - good, but how do I make sure no other bonds are added? And is this garuanteed not to change in the future? Can we introduce some sort of marker or command or whatever to establish a situation in which such a garuantee can be given? (That's what I liked about the "MathGraph" convention, it gave me that security.)
And, more specifically, I need this certainty in a format that can also be loaded into Jmol with inline models.
Getting and setting display states ... you've found the source of our misunderstanding there. The Jmol I knew did not offer a way of selecting an atom and changing settings for them. If there is no object storing "Style" settings unrelated to any part of the molecule than I understand you not feeling able to export style settings as an object, and I wouldn't want to ask you to - I'd have to live with that restriction. How about the checkboxes further down in the context menu, starting with "Axes" in the examples on "http://jmol.sourceforge.net/applet/";? I'll take anything you can easily put in a general "settings" object, not relating to any part of the molecule.
Let me again apologize for what I think was my main mistake: Making my requests based only on what I saw in the discussions, not on an actual attempt of working with a current Jmol version. I'm ready to make a start on that now, but it will be a slow process. So don't be distracted from your Xmas preparations (like I am now), you can answer the specific questions in this email at some convenient time. One thing I know from your last message is that the time is now right to start the actual work. That's perfect, I've also recovered my old sources to my current computer recently, so everything's coming together at the right time. I'm extremely grateful for your explanations.
Sebastian
(Jmol10pre4 is now loading in the background ...)
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