[Chimera-users] Moving atom labels

Eric Pettersen pett at cgl.ucsf.edu
Fri Aug 7 14:51:52 PDT 2009

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!



	Eric Pettersen
	UCSF Computer Graphics Lab

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