On Dec 18, 2008, at 2:28 PM, Huang, Shengyou wrote:
Is any way for Viewdock in Chimera to open a pdb file with NMR-style structures so that I can view those NMR-style structures one by one?
Yes, you can use ViewDock for that. When ViewDock asks you what the file type is, choose either "Dock 3 or 3.5", "Dock 3.5.x single", or "Dock 4, 5 or 6". Then the normal ViewDock interface will come up. There won't be much information in the various fields because an NMR PDB file doesn't have the embedded information that a DOCK output file does, but nonetheless you can click through the list of structures like normal. Another possibility is to open the NMR file as a trajectory (MD/ Ensemble Analysis->MD Movie) and play through the conformations that way. You could also use other analysis capabilities of the MD Movie tool, such as the RMSD map function. You might also want to try out the Ensemble Cluster tool, which will cluster your NMR ensemble and let you look at representative structures from each cluster. It sounds like you have a lot of conformations, so the Ensemble Match (compare your N structures in an NxN table) and Tile Structures (show all the conformations at once tiled in a grid on the screen) are probably not as useful as they would be for smaller ensembles. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hello, Just thought I would mention some related tutorials: The "trajectories/ensembles tutorial, part 2" includes viewing the NMR structure 1plx as a trajectory with MD Movie and calculating all-by- all RMSDs: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#pa...
The "model panel and ensembles" tutorial includes viewing NMR structures 1g1p and 1g1z, and using Ensemble Cluster and Ensemble Match: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html
There is also a ViewDock tutorial, but (naturally) it uses DOCK output, not an NMR structure. Best, 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 Dec 18, 2008, at 4:12 PM, Eric Pettersen wrote:
On Dec 18, 2008, at 2:28 PM, Huang, Shengyou wrote:
Is any way for Viewdock in Chimera to open a pdb file with NMR- style structures so that I can view those NMR-style structures one by one?
Yes, you can use ViewDock for that. When ViewDock asks you what the file type is, choose either "Dock 3 or 3.5", "Dock 3.5.x single", or "Dock 4, 5 or 6". Then the normal ViewDock interface will come up. There won't be much information in the various fields because an NMR PDB file doesn't have the embedded information that a DOCK output file does, but nonetheless you can click through the list of structures like normal.
Another possibility is to open the NMR file as a trajectory (MD/ Ensemble Analysis->MD Movie) and play through the conformations that way. You could also use other analysis capabilities of the MD Movie tool, such as the RMSD map function.
You might also want to try out the Ensemble Cluster tool, which will cluster your NMR ensemble and let you look at representative structures from each cluster.
It sounds like you have a lot of conformations, so the Ensemble Match (compare your N structures in an NxN table) and Tile Structures (show all the conformations at once tiled in a grid on the screen) are probably not as useful as they would be for smaller ensembles.
--Eric
participants (2)
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Elaine Meng -
Eric Pettersen