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?

Thanks,

Marla

On Fri, Jul 20, 2018 at 1:24 PM, Elaine Meng <meng@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@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