On Wednesday 29 October 2003 21:17, Miguel wrote: > > It is a while ago, and I am no longer working on that project, > > but you might remember me asking something similar in 2000. > > I only started working on Jmol code in 2003.
I should know, but I can't remember... Jmol is not the only thing I work on, and I tend to forget things I'm not working on fulltime... nothing personal. > > Out of sentimentality, I'm still lurking. I used an old version > > of the JMol Applet in a Java application I developed, and tried > > to make you aware of the fact that sometimes people calculate > > their own structures, complete with "final" bond and atom position > > information, and don't want a viewer program trying to be smart > > and decide where atoms and bonds should be. > > Certainly I agree 100%. Someone else also commented on this last week... Let me make clear that Jmol *does* have support for turning off automatic rebonding... Or did have. It might have gotten buried in all the recent work, but taking bond information from files is/has been available in Jmol. > What I believe I said in my email was: > - we use the connectivity in .mol files Indeed. > - we *need* to use the CONECT records in .pdb files It did... look in the cvs logs for the PDBReader, and you'll find that is was added at some stage, but removed later again, because the code was then not considered stable enough. > > Did I ever report back when I finished my project? You can see > > the results at "http://www.mathematik.uni-bielefeld.de/~CaGe/";. > > On the website, we praise JMol because the version we have does > > exactly what we want, but I don't know if that would still be > > true in the current version. What patches did you apply to make it 'leaner'? BTW, did you send those back to the Jmol project? I'm very interested in getting them (in some form) back into the main program... > Your web application would certainly need some modifications to run with > the current version of Jmol. > Probably over 90% of the Jmol code has been rewritten this year ... 100% > of the applet code. In the course of this we have explicitly dropped some > functionality from previous versions (like rendering styles). > > > My point is, I didn't get all I wanted from a standard version > > of the JMol Applet, so I ended up changing bits of the source > > code myself, using CML data with a new "Convention" of "MathGraph". I > > sent messages about my changes, but these seemed to get lost > > in the activies of JMol development. My apologies for that. Could you please resend them? > As I said, I only started working on the project this year. > If I missed a message of yours, then I apologize. > > I assure you, I *want* end-user feedback. > > > It would be good if a > > position such as mine wasn't completely forgotten. From that > > perspective, Miguel's response is not to the point. > > I am truly sorry if my response came across as 'arrogant' or not to the > point. Sebastian, please consider that the project is currently run by only two people. One of these (me) actually has a full time job next to it... It thus is very hard to give attention to all points of improvement of Jmol, and to not forget things... Ideally, things don't get forgotten, but this is very difficult with the small developers base Jmol has at this moment. > > My specific requirements were: > > * Exact representation of input data in terms of atom positions > > and bonds (Sometimes our bonds even were "impossible" from a > > chemistry point of view, but I still wanted JMol to faithfully show > > what it was given to show.) > > I agree 100% > > > I also needed this to be > > possible in CML, since that was the only format one could hand to > > the applet in a parameter. There was no scripting back then. > > > > * getter and setter methods for display settings (things like > > the drawing modes that existed back then) > > It isn't clear to me exactly what you are looking for, but I believe that > most of the this type of functionality should be available through the > scripting language today. > > > I dreamed of being able to always take the newest version and > > "plug it in" to my application, and I'd wonder if that could be > > made possible. > > > > Sebastian Lisken > > Sounds like you may have had some negative experiences with Jmol in the > past. > > There will be a major code base change with the upcoming v10 release. > Stability seems important to you. Therefore, I suggest you wait for the > Jmol v10 release and reevaluate it when it comes out. It it doesn't meet > your needs, then please let us know and we will add your requirements to > the list. Likewise. kind regards, Egon -- PhD Molecular Representation in Chemometrics Laboratory of Analytical Chemistry http://www-cac.sci.kun.nl/people/egonw.html ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
