[Chimera-users] Docking crystal structure in density map

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 14 13:21:45 PST 2009

Hi Andy,
Probably the adjustments to the coordinates caused them not be  
recognized as "helix" - however, you can force them to be labeled as  
helix as follows:

- select all the residues you want to be labeled as "helix"

(there are many different ways, and it depends on the details of your  
situation which is easiest... if your copies all have the same residue  
numbering, you could do something like use the command "select : 
43-57.a,103-119.b" which would select residues 43-57 in chain A and  
103-119 in chain B in all models... but there are many other possible  

- open the Selection Inspector (by clicking the greenish button on the  
bottom right corner of the Chimera window or choosing menu item  
Actions... Inspect)
   -- in that dialog, Inspect "Residue" and change "in helix" to "true"

I hope this helps,
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

On Jan 14, 2009, at 12:45 PM, Anindito Sen wrote:

> Dear All
> I have docked the crystal structure of a protein monomer manually in  
> the density map ( of a filament) and with some movements done with a  
> long alpha helix(part of the crystal structure) to make a decent  
> fit. However when I generated multiple copies of the docked  
> structure- regions where manual adjustments on the alpha helix were  
> made- came out like thin wires instead of being a ribbon.
> Thanks
> Andy

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