On Monday, October 11, 2010 12:31:13 pm Pavel Afonine wrote:
> Hi Ethan,
>
> > So far as I know, there is still no provision in phenix for reading in
> > existing TLS parameters. It always wants to regenerate them for itself.
>
> You are right, given suggested optimal selection for TLS groups
> phenix.refine is capcabale to do the rest as good as it can.
> There is simply no need to input any values of TLS values to phenix.refine
> since they will be determined based on actual reflection data and not user
> supplied B-factors)
You are missing the point.
What if you want to calculate Fcalc based on an existing model?
What if you want to explore application of the _same_ TLS model
to different sets of starting coordinates?
What if you want to read in a TLS description that was generated
through some other technique altogether, perhaps from trajectory
analysis of MD or NMA?
Any time you want to compare two alternative models, you need first
to be able to read them in.
It's all very well to say "the program knows best", but without the
ability to compare what the program picks to what an external tool picks,
how do you _know_ the program is "best".
Ethan
> , so just atom selections defining TLS groups is all
> phenix.refine needs. In one the next versions PHENIX will automatically
> determine the optimal TLS groups partitions as part of refinement and
> this is what will be used it in refinement.
>
> Cheers,
> Pavel.
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
