[Chimera-users] Rotamers

[Elaine Meng]

I would just like to caution everybody that "most probable" in this case is not the same as "best."  If you use swapaa without specifying criteria for choosing a rotamer, as in Angelica's example command, it will try to use the best rotamer for the specific situation.  As described in the "swapaa" manual page for the "criteria" option
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#options>

the default is to 
- first  choose the best fit to a density map if there is a density map (usually not)
- then choose the one with the least clashes with the rest of the structure
- then if a tie, choose the one with the most H-bonds with the rest of the structure
- then if still a tie, choose the one with the highest "probability"

The probability  only describes what is common in the database of structures used to make the rotamer library, and does not indicate what is really best given a specific location in a specific structure.  That is why we made the default method use clashes and H-bonds before the probability value.  If you really want to rely only on the probability value and not the specific structure, you can specify that with "criteria p" in the "swapaa" command.  Eric's new option will also use only the probability value, not clashes or H-bonding with the specific local environment.

Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 3, 2011, at 4:19 PM, Eric Pettersen wrote:

> 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