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

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 10 16:04:20 PDT 2007

Dear Ben,
Chimera doesn't have the ability to figure out for you the proper 
position of one copy relative to another.  You could open multiple 
copies, perform manual positioning, and then write out all the 
coordinates, but I imagine it might be difficult to get the right 
position of one copy relative to another, even manually/interactively.

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?

Yet another snag depends on how you will be using these coordinates. 
Does it require all the PDB files to be merged into one?  If so, can 
they be in a multi-MODEL form, or in a single model?  Chimera can 
output separate PDB files or a single multi-MODEL PDB file.  If you 
need all the coordinates to be in one model, however, you would have to 
edit the PDB output from Chimera so there are not atoms with duplicate 
atom numbers and chain IDs.  However, it all depends on what the *next* 
program you will be using requires and expects.  If you will just be 
using Chimera, however, no further editing would be required (in fact, 
you could just save a session rather than writing out coordinates).

Maybe someone else will have a smarter and less discouraging set of 
suggestions!  Best,

On Aug 10, 2007, at 12:53 PM, Ben Keshet wrote:

> Dear Chimera fans and team,
> I have a pdb file of a fragment of an amyloid fibril constructed of 8 
> layers
> (8 parallel strands of beta sheet).  I would like to overcome the end
> effects when modeling it, so I would like extend the existing 
> structure by
> duplicating it at its end.
> Does Chimera has a tool do the following: duplicate existing pdb 
> molecule
> coordinates, position the duplicated molecule at a desired location, 
> and
> then align it reasonably with respect to the original molecule?
> Thank you very much for your time and help.
> Ben

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