[Chimera-users] Feature suggestion - turn about pre-defined axis.

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 3 15:25:58 PDT 2015


This improvement applies to axes as defined by Axes/Planes/Centroids or the “define” command, with identifiers listed in the table of defined objects.

Just thought I should note that there is at least one command (measure rotation) that shows an “axis” that is a different animal, essentially 2 markers and a link.  However, since markers are implemented as atoms, you can already specify them as an atom pair in these rotation commands, most easily by selecting the two ends of the “axis” and using the word “sel” as the atomspec.

Elaine

> On Aug 3, 2015, at 3:06 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Okay, I have enhanced the axis argument for turn/rock/roll to also accepted the identifier for a defined axis.  Thanks for the suggestion!
> 
> —Eric
> 
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> 
>> On Aug 1, 2015, at 7:54 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
>> 
>> Hi all,
>> 
>> Just have a minor feature suggestion that I think would make the command “turn” more useful in certain circumstances. Currently, one can use “turn” to rotate about the x,y or z axes; an arbitrary vector; or about a bond or pair of selected atoms (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/turn.html).
>> 
>> Would it be possible for chimera to treat a predefined axis (e.g a helix axis, or the symmetry axis of an ion channel) as an atom-spec for the purposes of turn? As an example, “turn a1 45” would rotate 45 degrees about axis a1, with the default center of rotation corresponding to the midpoint of the axis. This would be very helpful for adjusting the relative orientations of symmetric oligomers, amongst other use cases.
>> 
>> Cheers,
>> Oliver.




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