>>My question regards the direction of the positive y axis of molecular >> model coordinates when rendered on the screen. > It is extremely important to get these right. Agreed
> In molecular structure > programs it is essential to get the handedness correct and these are > both right-handed as required. Yes, they are both right handed >>RasMol/Chime render the positive y axis going down (and positive z axis >> going away from the user and into the screen) Agreed >>Jmol renders the positive y axis going up (and positive z axis coming >> out of the screen and towards the user) Agreed >>This is problematic since I am trying to provide a smooth migration >> path from Chime to Jmol ... I assume that I will put in a user option. >> >>What do other molecular visualization programs do? > > ACD /3D appears to have +z INTO the screen > Weblab ViewerLite has z OUT of the screen > Mercury CCDC has Y INTO the screen > > JChempaint (and other editors must necessarily have Z OUT of the screen. > > So I doubt there is any real agreement other than the axes must be > right-handed. OK > Personally I would have the origin at bottom left (e.g. RasMOL-like) Hmmm ... I would have said that would put the origin at the upper left, since RasMol has the positive y axis going down. It won't be difficult for me to put in a user option to control this, so I guess that is what I will end up doing. For Jmol app users the option would be saved from session-to-session. For applet users there is a JmolApplet.properties file which sets default properties for the site. In addition, these properties can be overridden in the <PARAM ...> tags to the applet. There then comes the (somewhat less important) question as to what the default is. Let's see if other people have things to say. Miguel ------------------------------------------------------- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
