Hello. I have a problem with chimera! I want to combine two different pdb file by chimera , which will be merge into a single model. I used the "join models" section from chimera but the "apply" button was inactive and i don't know how i can activate it! please help me. thank you for your useful software.
Hello,
Why not use the "Copy/Combine" option under Favorites->Model Panel? You can then choose the models and combine them into a new one and save it.
On 30 July 2013 15:29, A Amiri atefeh_amiri23@yahoo.com wrote:
Hello. I have a problem with chimera! I want to combine two different pdb file by chimera , which will be merge into a single model. I used the "join models" section from chimera but the "apply" button was inactive and i don't know how i can activate it! please help me. thank you for your useful software.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hello, Join Models is for when you want to combine models AND make a covalent bond between them.
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
As explained in the link above, to use Join Models you must select two atoms in different models, each bonded to at most one other atom, to indicate where the bond should be formed, and enter values as needed to specify the geometry of bond formation (see the link for details). The Apply button won't be active until those things are done. (You can also see the manual by clicking the Help button on the dialog.)
However, if you just want to combine models and don't care about making a bond, you should instead use the "copy/combine" function in the Model Panel. Model Panel is in the menu under Favorites. Then you would have to choose the two models in the left side of the Model Panel to make the copy/combine button on the right side available. Or, you can use the "combine" command that has the same capabilities as the Model Panel function.
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 30, 2013, at 5:29 AM, A Amiri atefeh_amiri23@yahoo.com wrote:
Hello. I have a problem with chimera! I want to combine two different pdb file by chimera , which will be merge into a single model. I used the "join models" section from chimera but the "apply" button was inactive and i don't know how i can activate it! please help me. thank you for your useful software.
Hello again and thank you for helping. I exactly need the formation a covalent bond and because of that i used the Join Model option and although i studied the Building Structure part of manual i coudn't understand that how two atoms, that the bond should be formed between them, are selected. Please guide me more.Thanks.
________________________________ From: Elaine Meng meng@cgl.ucsf.edu To: A Amiri atefeh_amiri23@yahoo.com Cc: "chimera-users@cgl.ucsf.edu" chimera-users@cgl.ucsf.edu Sent: Tuesday, 30 July 2013, 10:22:22 Subject: Re: [Chimera-users] Hello
Hello,
Join Models is for when you want to combine models AND make a covalent bond between them.
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
As explained in the link above, to use Join Models you must select two atoms in different models, each bonded to at most one other atom, to indicate where the bond should be formed, and enter values as needed to specify the geometry of bond formation (see the link for details). The Apply button won't be active until those things are done. (You can also see the manual by clicking the Help button on the dialog.)
However, if you just want to combine models and don't care about making a bond, you should instead use the "copy/combine" function in the Model Panel. Model Panel is in the menu under Favorites. Then you would have to choose the two models in the left side of the Model Panel to make the copy/combine button on the right side available. Or, you can use the "combine" command that has the same capabilities as the Model Panel function.
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Jul 30, 2013, at 5:29 AM, A Amiri atefeh_amiri23@yahoo.com wrote:
Hello.
I have a problem with chimera! I want to combine two different pdb file by chimera , which will be merge into a single model.
I used the "join models" section from chimera but the "apply" button was inactive and i don't know how i can activate it!
please help me.
thank you for your useful software.
Hello, There are lots of ways to make Chimera selections, as described here: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html
One easy way is to do it with the mouse in the Chimera window. Ctrl-click on the first atom and Select-Ctrl-click on the second atom. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect
Of course to do that you have to display the atoms first, for example menu: Presets… Interactive 2 (all atoms)
You might try the "getting started" tutorial and other Chimera tutorials to become more familiar with selecting and other common tasks: http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 30, 2013, at 2:48 PM, A Amiri atefeh_amiri23@yahoo.com wrote:
Hello again and thank you for helping. I exactly need the formation a covalent bond and because of that i used the Join Model option and although i studied the Building Structure part of manual i coudn't understand that how two atoms, that the bond should be formed between them, are selected. Please guide me more.Thanks.
On Jul 30, 2013, at 3:36 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
One easy way is to do it with the mouse in the Chimera window. Ctrl-click on the first atom and Select-Ctrl-click on the second atom.
I think the last part should be Shift-Ctrl-click.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Yes, thanks to Eric for the correction! …. sometimes I can't think and type at the same time ... Elaine
On Jul 30, 2013, at 3:39 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
On Jul 30, 2013, at 3:36 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
One easy way is to do it with the mouse in the Chimera window. Ctrl-click on the first atom and Select-Ctrl-click on the second atom.
I think the last part should be Shift-Ctrl-click.
--Eric
participants (4)
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A Amiri -
Dan Cohen -
Elaine Meng -
Eric Pettersen