> In the course of scripting changes during an animation using a xyz file, > I would like to insert a monitor line between specific atoms in certain > models as an animation progresses.
Yes, that makes sense. > This is desireable because > animations in which molecular species move with respect to each other > may cease to show elongated bonds. Hmmm ... well I'm not sure that I agree with this usage of monitor. I think that it is a flaw to confuse 'bonds' with 'distance measurements'. I realize that this is the way one needed to do it in RasMol, but I believe that was a design flaw. Jmol does not render measurements the same way that it renders bonds. Bonds get drawn from the center of one atom to the next; measurements do not. Rather, measurements get drawn in front of the atoms involved, so that the user can see the endpoints and the distance (angle) value. > These could be designated by a short > script, such as: > > monitor x y > set monitors off > set monitors 0.1 > > Unfortunately, designating the desired models by: select (*/1, *2, *3, > etc.); does not seem to work. Curiously, the specified monitor line > appears only in the last frame (model) of the animation. True ... this is probably a mistake in Jmol. But, there are some problems in doing this ... related to backwards compatibility with existing scripts ... but let's save that for another discussion. > Can anyone > suggest a method of inserting monitor bonds in specified models of an > xyz animation? The correct solution is for us to create a new command that allows one to explicitly insert bonds under script control. This will sidestep the issue of how 'monitor' should behave. I will send a separate email on this topic. > A second question concerns the color of the monitor line. The default > color in Jmol is black, Actually, the default color of 'measurements' is black-or-white-contrast-with-existing-background-color. You are seeing black because you use a white background. If you use a black background then you see white. > but the Rasmol manual indicates the color should > be taken from the end point atoms. Jmol is not compatible with RasMol in this area. > I believe this would be preferable, > since the color monitors command would allow all other choices. What you want is a bond ... let's create a command that will do that. I'll send a separate email. Miguel ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnk&kid3432&bid#0486&dat1642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
