[Chimera-users] NMR-Style structures
pett at cgl.ucsf.edu
Thu Dec 18 16:12:45 PST 2008
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
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.
UCSF Computer Graphics Lab
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