Feature suggestion - turn about pre-defined axis.
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.
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@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. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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.
Fantastic, that was fast, thanks once again Eric! Cheers, Oliver.
On Aug 3, 2015, at 6:06 PM, Eric Pettersen <pett@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 <http://www.cgl.ucsf.edu/>
On Aug 1, 2015, at 7:54 AM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@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 <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. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Eric Pettersen -
Oliver Clarke