[Chimera-users] Connect and align duplicated models

Tom Goddard goddard at sonic.net
Tue Oct 11 15:42:11 PDT 2011

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



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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