How to place two identical proteins "near" each other
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
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
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
Hi Marla, It is difficult to answer specifically because I’m not sure from what you said whether your chains are all separate models or whether some models have more than one chain in them. Since you said you used the Model Panel to hide the ones you didn’t want, I’ll take a rough guess that each one is a separate model. In that case you could simply choose the same set of models as currently shown (“S” box checked in Model Panel) in the dialog from using menu:"File… Save PDB”. Or, using the Model Panel, you could close all the models you currently have hidden and then only the ones you want will be left. I also don’t understand why you couldn’t select. All the selection methods should work <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> As you have probably noticed, Chimera has a lot of stuff in it. The closest thing to “Chimera for dummies” is the “getting started” tutorial, but it might not cover the specific things you want to do. There are a couple versions of the getting started tutorial. This one is more self-contained and suitable for printing: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> …and this one in the User’s Guide covers the same things but with more links to the rest of the Guide, and split into two pages, one for menu and one for commands: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.h...> Besides that, you can scan through the titles of the other tutorials <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> ...and the general usage topics in the User Guide (e.g. “superimposing structures”, “modifying and saving data”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecore.html> ...to see if any of them sound similar to the things you are trying to do. There is also menu: "Help… Search Documentation” to look for specific topics. 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 24, 2018, at 10:10 AM, Marla DeKlotz <mdeklotz@gmail.com> wrote:
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
participants (2)
-
Elaine Meng -
Marla DeKlotz