[Chimera-users] Display all rotamers

Elaine Meng meng at cgl.ucsf.edu
Sat Dec 6 11:04:19 PST 2008

On Dec 6, 2008, at 9:35 AM, daniel.hilger at lrz.uni-muenchen.de wrote:
> I´m really sorry for my imprecise question. I will concretize it. I  
> know
> the rotamer tool, but I don´t want to replace only one rotamer into
> another. I will have them all in the structure and in the according
> pdb-file. With the rotamer tool, it is only allowed to choose one  
> rotamer
> out of the rotamer list before clicking "Apply". This is my problem,  
> and I
> didn´t found an appropriate answer in the manual and help menu.

Hi Daniel,
I'm sorry for misunderstanding -

It's true that Apply only puts one copy in the structure, but if you  
don't Apply and simply keep the Rotamer list dialog and choose all of  
its lines, that displays all of the rotamers at the same time.  Maybe  
that would allow you to do what you want. The Rotamer list dialog  
allows calculating clashes and H-bonds, plus selecting the rotamer  
atoms so you can control their appearance with the Actions menu.

The issue is that the structure can't have multiple indistinguishable  
atoms (with the same name and residue number).  We have talked about  
allowing multiple rotamers to be applied to the structure by giving  
them different "alternate location" ID codes, but that has not been  
implemented yet.  Also, some residues may have more rotamers than the  
number of possible alternate location ID codes.  Nevertheless we will  
make sure it is on one of our requested features lists.

So currently you can't save PDB with multiple rotamers, but you can  
save/restore the session in the state where all of the rotamers are  
I hope this helps,

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