[phenixbb] mutate to polyAla in phenix.automr?

Randy Read rjr27 at cam.ac.uk
Fri May 8 03:38:50 PDT 2009


We are adding various model preparation utilities for the MR pipelines  
in Phenix, and they will appear fairly soon.  If you really want a  
polyAla model, it will be possible to trick the tools into doing this  
for you (e.g. by making an alignment file that has all Ala for your  
target).  However, I personally do not believe in using polyAla  
models.  (If there are clear examples of where this is the best  
option, I'd be pleased to hear about them.)  I prefer the  
Schwarzenbacher et al approach of trimming non-identical sidechains  
back to Ala but leaving the identical ones alone.


Randy Read

On 7 May 2009, at 15:01, Francis E Reyes wrote:

> Is there an option or a phenix.* utility to mutate a MR model to poly
> ALA before the MR is done?
> Thanks!
> FR
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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