[phenixbb] mutate to polyAla in phenix.automr?
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.
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?
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
> phenixbb mailing list
> phenixbb at phenix-online.org
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
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