[Chimera-users] NMR-Style structures

[Elaine Meng]

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#part2 
 >

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 at 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
>