Hi Joe, Elaine's suggestion is the way to go. If you have two copies of your molecule #0 and #1 and you want to add additional subunits use the "measure rotation" and the sym commands to do it. Here's an example. Notice I take the axis, axis point, rotation angle, and shift along axis from the measure rotation and use those in the "sym" command to create 4 additional copies using helical symmetry. A single rotation and translation always specifies a helical symmetry (rotation about an axis and shift along that axis). In the case where the shift along the axis is 0 you get cyclic symmetry. You'll probably find the "sym" command documentation useful http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html Tom measure rotation #0 #1 Reply log: Position of 1E6J (#1) relative to 1E6J (#0) coordinates: Matrix rotation and translation 0.96949029 -0.23745478 -0.06085881 98.69560733 0.03663564 0.38584119 -0.92183752 7.88875940 0.24237657 0.89148292 0.38276860 7.78837497 Axis 0.97552284 -0.16313335 0.14745407 Axis point 0.00000000 17.01960113 14.23231084 Rotation angle (degrees) 68.34295730 Shift along axis 96.14132684 sym #1 group h,96.14,68.34,5 axis 0.9755,-0.1631,0.14745 center 0,17.02,14.23 coord #0
Hi Joe, Hmm, well, you could measure the transformation between your first and second copies with "measure rotation." Then, if that corresponds to some symmetry group or product of groups, you could generate multiple additional copies with a single "sym" command using the "group" option.
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
However, I'm not sure how easy or difficult it would be to figure out the necessary sym command from the information given in the Reply Log from the measure command, i.e. whether it is a simple helical relationship or something more complicated. Maybe a python script to repeatedly apply the transformation to additional copies would be more effective (beyond my skill set, sorry).
I'm not the most knowledgable here on this particular topic; perhaps the others will have clearer ideas of how to attack the problem, or a script. Best, 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 Oct 11, 2011, at 1:04 PM, Joe Ping-Lin Hsiao wrote:
Hi, I are trying to use Chimera to produce duplicates of one fibrinogen, rotate and move them, and concatenate together in a certain way. The fibrinogen looks like this (http://dl.dropbox.com/u/3757507/chimera1.png). I want to duplicate the model, and connect them in a chain (http://dl.dropbox.com/u/3757507/chimera2.png). The second image shows only two instances, but there will be more.
Currently I do it by hand, including rotating and aligning them in correct z positions. But it take a lot of time to do it because the duplicates generated by using Tools/Higher-order structure/Unit Cell are not in the same plane. I have to look back and forth in different directions to make sure them are aligned. So I are wondering is there any way to automate this process, such as apply the previous transformation to a new duplicate?
Thanks, Joe
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