question about chimerax
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 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 <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. 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 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%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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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.ucsf.edu%2Fmailman%2Flistinfo%2Fchimerax-users&data=01%7C01%7CFEF13%40pitt.edu%7C09faa9032f234682baef08d5fd846272%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=RRHd61fhF6j5Mc6hoDmkB3%2BpBUFElbq3Q00%2FHXXkCSY%3D&reserved=0
Hi Fei, Oh, the bracket symbols [ ] should not be included in your command. They just mean that the keyword and value are optional and could be omitted if the default is what you want. For example, an image-saving command could be: save /Users/meng/Desktop/proteasome.tiff transparent true The size would be the same as your graphics window, and the format is known from the output filename. The defaults are described in the manual: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#image> This page explains the meanings of brackets and fonts in the command usage descriptions: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.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 Aug 14, 2018, at 8:49 AM, Fang, Fei <FEF13@pitt.edu> wrote:
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
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
participants (3)
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Elaine Meng -
Fang, Fei -
Tom Goddard