hi-ho Miguel,
On 2004-10-14 (18:02) Miguel wrote: >Tim & Miguel wrote: > >>>>I am working with the monitors in JmolApplet v10pre14a. The >>>>monitor lines only work when the residues that contain the atoms >>>>being measured are in wireframe or spacefill - they do not show >>>>up in backbone or cartoon. is this a bug that you can easily fix? >>> <snip> >>more info - this monitors bug only appears to affect 'cartoon' >>shapes. if I do this in 1CRN, the monitor works fine: > >I think this was intended to be a feature, not a bug. > >A measurement is for measuring distances or angles. > >Therefore, when measurements are drawn all of the points that they >are measuring must be visible. > specifically, I am trying to draw monitors between alpha carbons in a protein, rendered as backbone (or cartoon). so maybe this becomes a philisophical question now - are the alpha carbons 'visible' when the render style is cartoon or backbone? for now, I worked around this by rendering the alpha carbons in spacefill 0.1, which seems to work ok. it's a kludge, but if the alternative is an ugly amount of recoding I can deal with it NBD. if I had to choose, I'd rather see the monitor lines run to the center of the atom ;-) > >>same deal if I use cartoon instead of backbone. maybe turning off >>the 'real' shapes (atoms and bonds) also turns off the monitor >>lines? > >Correct. > >If you turn off any of the points then the measurement is not drawn. > >>btw, this is reverse of RasMol - turning off everything still >>leaves monitors, hbonds, and ssbonds. these must be turned off >>explicitly. > >Q: So, is it the case that you are asking that all measurements be >drawn all the time, regardless of whether or not the atoms are >shown? > well, I don't know. I was speaking to the issue of backwards compatibility. my personal opinion is no, monitors should not be visible if the atoms are not. but it might be an argument for two commands in Jmol - monitor and measure - as you mentioned a while back, Miguel. measure would be a Jmol-enhanced version of monitor. monitors would run to the center of the atoms, and by independent of atom visibility. again, for me these are minor issues. :-) regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
