[chimera-dev] How to use "getRotamers" function?

[Eric Pettersen]

On Jul 20, 2009, at 10:37 PM, ylei at ecs.umass.edu wrote:

> Hi all
>
> I'm trying to get the rotamers for the given residue along the
> backbone using Dunbrack Backbone Dependent Library. So far, I want to
> use getRotamers function. But when running this command in the python
> shell, I got this error "No module named Dunbrack". I don't know if
> there is a module "Dunbrack" which I should import first.

I guess I need more details about how you tried to "use" the  
getRotamers function.  Were you using Chimera's IDLE interpreter?   
Your own version of Python?  What was the code exactly?

> Moreover, besides getRotamers, there are several other functions, e.g.
> getRotamerParams, extractResInfo, useRotamer, RotamerLibraryInfo,
> registerLibrary, useBestRotamers, etc and a class called RotamerParams
> in the same file. I also found there are two associated functions in
> the Dunbrack folder, say, dependentRotamerParams and
> independentRotamerParams, which are used in the above functions.
>
> Can someone help me distinguish these functions? Which one will be
> useful if I need a full set of rotamers for certain purpose (i.e.
> side-chain structure prediction) given the backbone?

Here's a brief rundown on what the functions you listed do:

getRotamers:  Takes a Residue instance and optionally phi/psi angles  
(if different from the Residue), residue type (e.g. "TYR"), and/or  
rotamer library name.  Returns a boolean and a list of Molecule  
instances.  The boolean indicates whether the rotamers are backbone  
dependent.  The Molecules are each a single residue (a rotamer) and  
are in descending probability order.  Each has an attribute  
"rotamerProb" for the probability and "chis" for the chi angles.

getRotamersParams:  Takes either a Residue instance or a residue type  
and optionally phi and psi angles (if omitted and a Residue instance  
was given, then that Residue's phi/psi will be used).  Returns a  
boolean and a list of RotamerParams (in descending probability  
order).  The boolean indicates if the rotamers are backbone  
dependent.  RotamersParams is a simple container class that has an  
attribute 'p' for probability and 'chis' for a list of chi angles.   
Most of this is covered in the getRotamerParams doc string.

extractResInfo:  Takes a Residue instance.  Returns the residue type,  
phi, psi, and "cis" or "trans".

useRotamer:  Takes a Residue instance and a list of one or more  
rotamers (as returned by getRotamers) and swaps the Residue's side  
chain with the given rotamers.  If more than one rotamer is in the  
list, then alt locs will be used to distinguish the different side  
chains.

RotamerLibraryInfo:  a class that holds information about a rotamer  
library:  how to import it, what citation to display, etc.

registerLibrary:  Takes a string indicated the "import name" of a  
library (i.e. what name to use in an import statement) and adds a  
RotamerLibraryInfo instance for it to the list of known rotamer  
libraries ("Rotamers.libraries").

useBestRotamers:  the implementation of the "swapaa" command.  If you  
look at the documentation for that command I think this method's  
arguments and actions will be mostly self-explanatory.  The only  
slight exception is that the 'targets' argument is a list of Residue  
instances.

I hope this helps.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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