[Chimera-users] How to place two identical proteins "near" each other

Marla DeKlotz mdeklotz at gmail.com
Tue Jul 24 10:10:54 PDT 2018

Hi Elaine,
I'm trying to switch tactics and take an existing pdb of the full structure
(I'm working with a capsid protein that forms a icosahedron), select just
the chains that make up one pentamer, and write that selection as its own
pdb.  I can't figure out how to do any of that.  I got chimera to display
just the 5 trimers that I want by painstaking unclicking every other chain
in the model panel.  But it won't write a pdb of just those chains.

I'm having a lot of trouble with chimera in general.  I typically can't
find how to do what I want to do in the program menus and the help pages
are difficult to navigate and give a lot of detail that I don't want at
this point.  Is there more of a "chimera for dummies" resource anywhere?


On Fri, Jul 20, 2018 at 1:24 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Marla,
> Actually Chimera’s “tile” is not just a tile view, it actually puts
> structures in separate locations.
> However, one can of course move a structure without moving the others.
> You can “freeze” any structure so that it ignores mouse manipulations, by
> deactivating it (for example, unchecking the “A” button in Model Panel
> opened from Favorites menu).
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
> For more precise operations, you can specify in commands which models to
> move.  See the commands “move” (translation),  “turn” (rotation), etc. with
> the “models” option.  For example, to get side-by-side comparisons, I first
> superimpose the models so that they’ll be in a certain orientation and then
> translate them apart:
> move x -20 mod #0
> move x 20 mod #1
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Jul 20, 2018, at 10:25 AM, Marla DeKlotz <mdeklotz at gmail.com> wrote:
> >
> > I am trying to prepare a pdb to use in Rosetta docking.  I need to place
> two copies of the same protein "near" each other, in roughly the alignment
> they should have after they dock together.  Chimera seems to always overlay
> the two copies and I can't figure out a way to separate them and
> move/rotate each one independently.  I don't want a tile view, I need them
> to have a real relationship in space so Rosetta knows where to "aim" its
> docking protocol.
> >
> > Thanks,
> > Marla
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