[Chimera-users] question about annealing residues in pdb file

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 31 15:14:05 PDT 2006

Hi Sanket,
If I am understanding the problem correctly, it's easy to fix; just  
use the command "longbond".

Chimera shows the connections because the PDB file (I am guessing)  
still implies they are there: the residues are in the same chain and  
don't have TER between them.  DeepView probably applies some distance  
test similar to "longbond" automatically when a structure is opened.
I hope this helps,

On Aug 31, 2006, at 1:21 PM, Shah, Sanket S wrote:

> Hello,
> I have been using chimera extensively for pdb rendering and  
> manipulation. I needed some information that i couldn't find in the  
> archives. I am aware that chimera displays the pdb file according  
> to the co-ordinates mentioned in the pdb file. However in my  
> situation I have changed co-ordinates of some of the secondary  
> structure elements like helices to do a better fit. and I have  
> saved the new coordinates in the same pdb file. So now when i  
> render this pdb file it shows me the structure with the modified  
> orientation, however chimera displays a continuous model. In the  
> sense, the breaks that I had introduced by changing the angles of  
> some of the helices and thus making the linkage discontinuous are  
> somehow annealed by chimera. So my question is what sort of  
> algorithm chimera employs to seal breaks in the pdb structure. The  
> same pdb strucutre when viewed in swiss model deepview software  
> contains gaps/breaks at the junctions where the coordinates of the  
> helices have been modified!
>   from the original ones. however no such breaks are seen when  
> displayed through chimera. First I thought chimera does energy  
> minimization to find out the best way to arrange the loops between  
> the helices so as to create the best continuous structure. However  
> it seems that chimera doesn't do energy minimization, yet it's able  
> to display a complete structure. Could you please inform me about  
> how this is accomplished.
> Thanks
> Sanket
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Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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