Hi Mike, On Aug 6, 2009, at 6:02 PM, Michael Day wrote:
How does one change the position of atom labels? For small coordination complexes the default atom labels land on the atom and it would be nice to move them as a whole or individually so they are alongside the atom ball or anisotropic ellipsoid.
For the 1.4 release we hope to have label repositioning with the mouse available (as listed on this Wiki page: http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Release1.4) . We don't have it yet. However, the underlying mechanism is in place and I have modified Thermal Ellipsoids to offset atom labels by an amount equal to the longest half-axis of the atom's displayed ellipsoid. That will be in tomorrow's build. Furthermore, I made it so that you can set the label-offset attribute with the "setattr" command. This required some mods to that command since the label-offset attribute is a vector and the setattr command didn't support non-scalar values. So in tomorrow's build this command will move selected atom's labels half an angstrom to the right: setattr a labelOffset 0.5,0,0 sel It's not 100% certain that this is how setting vector attributes will work in the 1.4 release, but if it changes I'll let people know.
While I'm on the ellipsoid topic; has there been progress on overlaying axis on the ellipsoids? I know I originally asked about axis and shaded octants but after using the anisotropic option for the last month or so I notice tat there is a tremendous amount of information conveyed with just the color and shape and shaded octants may not add much information (in fact it may just confuse the issue).
Well....no, not really. I've had a lot of my time tied up with system administration issues related to a new Linux cluster we're converting over to (principally getting an efficient reliable backup system implemented), but the good news is that that time commitment is winding down and I will have more time for issues such as these that I would prefer to work on. So hopefully soon. The only thing I've managed to do is get some of the underlying infrastructure for the probability calculator done (basically conscripting a Simpson's Rule numerical integrator once I understood what I needed).
Your implementation of thermal ellipsoids is very, very useful!
Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab