[Chimera-users] Connect and align duplicated models

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 11 14:28:33 PDT 2011

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.


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 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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