[Chimera-users] transposing a pdb structure ("copy & paste")

Eric Pettersen pett at cgl.ucsf.edu
Fri Aug 10 16:53:36 PDT 2007

On Aug 10, 2007, at 4:04 PM, Elaine Meng wrote:

> To manually position a structure relative to another, you could
> interactively rotate/translate and/or use the "move" (translation) and
> "turn" (rotation) commands.  You can freeze/unfreeze a copy using the
> Active checkbox in the Model Panel (in the Favorites menu by default),
> the command "select," or the little checkboxes under the Command Line
> (also under Favorites).
> If you did manage to position copy 2 relative to copy 1 to your  
> liking,
> you could write the transformation matrices out (see "matrixget"
> command).  From those you could calculate the transformation of 2
> relative to 1 and also generate appropriate matrices that would then
> position 3, 4, ... correctly (see "matrixset" command).  I admit I
> don't know how to do those calculations.  Anyone?

It's a little tricky.  Basically, you want to get copy 1's matrix to  
be the identity matrix while keeping copy 2 in the same relative  
position.  Here's one way to do it (and maybe someone can suggest  
something better):

1) open yet another copy (copy 3) as a reference
2) use "matrixset" to set copy 3's matrix to be the identity matrix
3) use the "match" command with the 'active' keyword to match copy 1  
onto the reference (copy 3) while also moving copy 2 appropriately
4) use "matrixget" to get copy 2's new transformation matrix

I would imagine that copy 2's matrix is essentially all translation  
components (i.e. the upper 3x3 is all zeroes or near-zeroes) so all  
you need to do to place additional copies to multiply the translation  
components by 2, 3, etc.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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