[Chimera-users] Moving atom labels
pett at cgl.ucsf.edu
Fri Aug 7 14:51:52 PDT 2009
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!
UCSF Computer Graphics Lab
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