I forgot to say: another possibility instead of using "align" is to display the helix axis as a cylinder with the "define" command or the "Axes/Planes/Centroids" tool and then orient the axis by hand. It may be easiest to do this along Z so you are looking at the end of the cylinder, then use "turn" as before to align along different axes. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> example: open 1gcn define axis perHelix true Elaine On Feb 8, 2010, at 9:28 AM, Elaine Meng wrote:
Hi S, As described in this recent post, <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004768.html
you can use the "align" command to put one or more atoms in front and one or more atoms in back (aligns them along the Z axis in the center of the screen), then use "turn" to rotate the alignment to other axes.
For example, including 3 different possibilities for "align":
open 1gcn rlabel align :1.a :29.a ( - OR - ) align :1.a@n :29.a@c ( - OR - ) align :1.a@n,ca,c :29.a@n,ca,c turn y 90 focus
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2010, at 8:52 AM, snoze pa wrote:
Dear Chimera Users,
I am wondering if it is possible to align the molecule along the X-Y or Z axis. I want to place the molecule, along a line joining N to C terminal line. Idea is to place a molecule along this line(N to C line) which is X or Y or Z axis.
Thank you,
S
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