[Chimera-users] Rotamers in Chimera
pett at cgl.ucsf.edu
Tue May 31 17:28:53 PDT 2016
Unfortunately, the 2011 Dunbrack library is not freely redistributable, so we can’t just drop it into Chimera. There have been some informal discussions with the Dunbrack lab about allowing redistribution in this case, but nothing has happened so far.
If the 2011 library has the exact same layout as the 2002 library then there’s some hope that a non-expert Chimera programmer could incorporate the library themselves. The 2011 library would need files corresponding to the backbone-dependent 2002 file (bbdep02.May.sortlib) and independent file (bbind02.May.lib) and in the exact same format (or at least a very similar format). Otherwise the conversion would be pretty challenging. My hazy recollection of looking at the 2011 library was that this wasn’t the case, but I could be mis-remembering.
If the 2011 library is similar enough, the basic outline of what would need to be done is:
1) Pull the Chimera source code from our svn repository, so that you can access the Python library-processing scripts that aren’t included in the app distribution.
2) Use slightly-modified versions of the prepdeplib.py and prepindlib.py scripts in Rotamers/Dunbrack to create dependentRotamerData.zip and independentRotamerData.zip files.
3) Create a new subdirectory of Rotamers (Dunbrack11?) to hold these files along with an __init__.py that would be very similar to Dunbrack/__init__.py
4) Modify Rotamers/__init__.py to register the new library with Chimera.
You can see that even the “easy” conversion is a fair bit of effort. If the library formats aren’t similar, then you probably need a Python expert to modify the prep***lib.py scripts to process the 2011 library files into the corresponding zip files.
UCSF Computer Graphics Lab
> On May 28, 2016, at 12:19 PM, Lew Jacobson <ljac at pitt.edu> wrote:
> I am using Chmiera 1.10 build 40304 on a Mac. (I am a leftover Midas user!)
> So far as I can tell, this version is still using the Dunbrack 2002 rotamer library. Is any subsequent version using the improved 2011 Dunbrack library? If not, can you instruct me how to incorporate that newer library into Chimera?
> Lew Jacobson
> Dr. Lewis Jacobson
> Professor of Biological Sciences
> Univ. of Pittsburgh
> Pittsburgh PA 15260
> Fax 412-624-4759
> LJAC at pitt.edu
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
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