Flipping between alternate conformations (depiction/movie)
Dear Chimera team, Is there a movie command that can easily depict the interconversion between two alternate conformations in a nucleic acid or protein residue (designated conformation a and b) within a pdb file. I am really trying to illustrate with a movie how the phosphates flip between two well defined states in an ultra-high resolution DNA crystal structure using a chimera movie. Thanks in advance, Dave Chenoweth ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen@caltech.edu **********************************************
Hi Dave, The Morph Conformations tool (under Tools... Structure Comparison) generates interpolated intermediate structures and then opens the result as a trajectory in the MD Movie tool. With MD Movie you can interactively play the trajectory but also save a movie file. These are not in command form, however. Take a look and see if these tools allow you to do what you want... Morph Conformations: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html
MD Movie: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.ht...
Tutorials with morphing examples: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html
Tutorial that includes saving a movie with MD Movie: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#pa...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 19, 2008, at 11:11 AM, David Chenoweth wrote:
Dear Chimera team,
Is there a movie command that can easily depict the interconversion between two alternate conformations in a nucleic acid or protein residue (designated conformation a and b) within a pdb file. I am really trying to illustrate with a movie how the phosphates flip between two well defined states in an ultra-high resolution DNA crystal structure using a chimera movie.
Thanks in advance, Dave Chenoweth
Actually, Morph Conformations has a bug right now in showing altlocs. You need to make two copies of your PDB and in one strip the B locations of that residue and the replace the 'A' indicator letters with blanks, and in the other do the converse. If you open those two files you should be able to morph between them as Elaine describes. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Aug 19, 2008, at 11:26 AM, Elaine Meng wrote:
Hi Dave, The Morph Conformations tool (under Tools... Structure Comparison) generates interpolated intermediate structures and then opens the result as a trajectory in the MD Movie tool. With MD Movie you can interactively play the trajectory but also save a movie file.
These are not in command form, however. Take a look and see if these tools allow you to do what you want...
Morph Conformations: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html
MD Movie: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.ht...
Tutorials with morphing examples: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html
Tutorial that includes saving a movie with MD Movie: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#pa...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Aug 19, 2008, at 11:11 AM, David Chenoweth wrote:
Dear Chimera team,
Is there a movie command that can easily depict the interconversion between two alternate conformations in a nucleic acid or protein residue (designated conformation a and b) within a pdb file. I am really trying to illustrate with a movie how the phosphates flip between two well defined states in an ultra-high resolution DNA crystal structure using a chimera movie.
Thanks in advance, Dave Chenoweth
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Hi Dave, I was assuming you wanted to morph between the positions. If instead you simply want to jump from one to the other, you can just use the display command. For example, if both are shown then "~disp @.b" would hide the B altlocs. Then you could switch with "disp @.b; ~disp @.a" (the semicolon prevents display of the intermediate state with both shown). You could include the residue number and chain ID in these commands, for example :335.a@.b refers to altloc B atoms of residue 335 in chain A. Best, Elaine On Aug 19, 2008, at 11:11 AM, David Chenoweth wrote:
Dear Chimera team,
Is there a movie command that can easily depict the interconversion between two alternate conformations in a nucleic acid or protein residue (designated conformation a and b) within a pdb file. I am really trying to illustrate with a movie how the phosphates flip between two well defined states in an ultra-high resolution DNA crystal structure using a chimera movie.
Thanks in advance, Dave Chenoweth
Elaine and Eric, Morph Conformations worked great after a little PDB editing. Thanks for your help! -Dave On Aug 19, 2008, at 12:11 PM, Elaine Meng wrote:
Hi Dave, I was assuming you wanted to morph between the positions. If instead you simply want to jump from one to the other, you can just use the display command. For example, if both are shown then "~disp @.b" would hide the B altlocs. Then you could switch with "disp @.b; ~disp @.a" (the semicolon prevents display of the intermediate state with both shown). You could include the residue number and chain ID in these commands, for example :335.a@.b refers to altloc B atoms of residue 335 in chain A. Best, Elaine
On Aug 19, 2008, at 11:11 AM, David Chenoweth wrote:
Dear Chimera team,
Is there a movie command that can easily depict the interconversion between two alternate conformations in a nucleic acid or protein residue (designated conformation a and b) within a pdb file. I am really trying to illustrate with a movie how the phosphates flip between two well defined states in an ultra-high resolution DNA crystal structure using a chimera movie.
Thanks in advance, Dave Chenoweth
participants (3)
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David Chenoweth -
Elaine Meng -
Eric Pettersen