[Chimera-users] Rotamers

Eric Pettersen pett at cgl.ucsf.edu
Thu Feb 3 16:19:34 PST 2011

On Feb 2, 2011, at 11:03 AM, Angelica Nakagawa Lima wrote:

> Hi
> I can get the rotamers if I use the graphical version (when I click  
> in tools -> Structure Editing -> rotamers). But I would like to do  
> same thing  with  the comands.
> I used the comand swapaa (swapaa ile :10.a) and I write the pdb with  
> the ile's rotamer (the most probable), however I would like to write  
> the pdb file with the second most probable rotamer too.
> How do I do this?

Hi Angelica,
	I've implemented an enhancement that will be available in tomorrow's  
1.6 daily build that may or may not solve your problem.  The change is  
that if in the swapaa command you specify an integer N as the  
"criteria" value then the Nth most probable rotamer will be used.  So  
a criteria of 2 will use the second most probable rotamer, 1 will use  
the most probable (same as 'p'), 14 the 14th most probable, etc.  You  
cannot mix integer criteria with the letter criteria.
	So I think this addresses your problem if you wanted to write one  
file with the most-probable rotamer, and another file with the second- 
most-probable one.  If you wanted to write one file with both rotamers  
(using alt locs) then this change doesn't help but there may or may  
not be something I can do about that. -- let me know if that's the case.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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