[Chimera-users] NMR-Style structures

Eric Pettersen 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  
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 Pettersen
                         UCSF Computer Graphics Lab

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