Hi Elaine,

Thanks for your kindly reply. I have two protein complexes, one is 12 from pdbdev, the other one is pdb code: 4cr4. When I opened the two complex one by one, the two proteins bind, and I can't move them by each other, even by selecting one of them. I'm not sure it's because the two protein complexes are too large or else. I'll appreciate it if you can help me solving the problem. Thanks.

Best,

Fei

________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, August 8, 2018 4:03:13 PM To: Fang, Fei Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] question about chimerax

Hi Fei, Re: moving models separately

You can select part of the model (Ctrl-click) you want to move, and then use the mouse mode to “translate selected models” or “rotate selected models”… the unselected ones will not be affected by that mouse button. If you use the icons on the left side of the window to assign the function to the mouse, that assigns only “button 3” (right button), but you can use the “mousemode” command to assign any button, optionally in combination with some other key like Shift.

https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fmousemodes.html&data=01%7C01%7CFEF13%40pitt.edu%7C8a7dc5dceec54457950b08d5fd69f92d%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=mHpR%2FBSCRS9dWlVrPhGz2JLpcpKWKINTesdzqYuJiyI%3D&reserved=0 https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fui.html%23mousemode&data=01%7C01%7CFEF13%40pitt.edu%7C8a7dc5dceec54457950b08d5fd69f92d%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=TovIlLfd1yvV3TdpxYKN8JYvMsTv0qEMxW6Ma7R5wJA%3D&reserved=0

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Aug 8, 2018, at 8:54 AM, Fang, Fei FEF13@pitt.edu wrote:

Hi, This is Fei from University of Pittsburgh. Here is a question about chimera x. By introducing two structures into the chimera x, how can I move the one structure over so that they're no longer covering each other? Thanks. Best, Fei

Hi Elaine,

Thanks for your kindly reply, and I can move the object I want to move with your suggestion. BTW, when I want to save the image of the result by using save command line, "save [ image ] proteasome [ format tiff ] [models #1] [[ width 2457 ][ height 3000 ]| pixelSize 0.4] [ supersample 3 ] [ quality 95 ] [ transparentBackground true ] ", there is a warning of "Expected a models specifier or a keyword". Any advice? Thanks a lot.

Best,

Fei

________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, August 8, 2018 7:12:15 PM To: Fang, Fei Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] question about chimerax

Hi Fei, Just selecting is not enough. You also have to turn on one of the mouse modes to move only the selected protein, by clicking on the icon for that mousemode (see link I gave before) or using the “mousemode” command.

Or, without doing any selecting, you can just use the “move” command with the “model” option to specify which model to move, as suggested by Tom. Elaine

On Aug 8, 2018, at 1:19 PM, Fang, Fei FEF13@pitt.edu wrote:

Hi Elaine,

Thanks for your kindly reply. I have two protein complexes, one is 12 from pdbdev, the other one is pdb code: 4cr4. When I opened the two complex one by one, the two proteins bind, and I can't move them by each other, even by selecting one of them. I'm not sure it's because the two protein complexes are too large or else. I'll appreciate it if you can help me solving the problem. Thanks.

Best, Fei From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, August 8, 2018 4:03:13 PM To: Fang, Fei Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] question about chimerax

Hi Fei, Re: moving models separately

You can select part of the model (Ctrl-click) you want to move, and then use the mouse mode to “translate selected models” or “rotate selected models”… the unselected ones will not be affected by that mouse button. If you use the icons on the left side of the window to assign the function to the mouse, that assigns only “button 3” (right button), but you can use the “mousemode” command to assign any button, optionally in combination with some other key like Shift.

https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fmousemodes.html&data=01%7C01%7CFEF13%40pitt.edu%7C09faa9032f234682baef08d5fd846272%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=e7HBpYKVjle1CM5AD9glFOZYEJrt5zr8JRNJ96OI8kg%3D&reserved=0 https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fui.html%23mousemode&data=01%7C01%7CFEF13%40pitt.edu%7C09faa9032f234682baef08d5fd846272%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=M5UaDmr%2F8d7xqpQwPIYxTrudSlhZW7vcnpbIT7BAh0U%3D&reserved=0

I hope this helps, Elaine

---

Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Aug 8, 2018, at 8:54 AM, Fang, Fei FEF13@pitt.edu wrote:

Hi, This is Fei from University of Pittsburgh. Here is a question about chimera x. By introducing two structures into the chimera x, how can I move the one structure over so that they're no longer covering each other? Thanks. Best, Fei

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.uc...

For more precise movement you can use a command.

move x 10 model #2

or

move 10,0,0 model #2

will move model #2 by 10 Angstroms along the screen x axis. You can also move along the x-axis of the molecule coordinate system with

move 10,0,0 model #2 coordinateSystem #2

Tom

On Aug 8, 2018, at 1:03 PM, Elaine Meng wrote:

Hi Fei, Re: moving models separately

You can select part of the model (Ctrl-click) you want to move, and then use the mouse mode to “translate selected models” or “rotate selected models”… the unselected ones will not be affected by that mouse button. If you use the icons on the left side of the window to assign the function to the mouse, that assigns only “button 3” (right button), but you can use the “mousemode” command to assign any button, optionally in combination with some other key like Shift.

http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode

I hope this helps, Elaine

---

Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Aug 8, 2018, at 8:54 AM, Fang, Fei wrote:

Hi, This is Fei from University of Pittsburgh. Here is a question about chimera x. By introducing two structures into the chimera x, how can I move the one structure over so that they're no longer covering each other? Thanks. Best, Fei

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users