[phenixbb] --unused_ok, .def, documentation,...

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Tue May 12 05:36:09 PDT 2009

Couple of comments:

>I keep seeing people having trouble refining their structures in
phenix.refine just because they were using "-->unused-ok" option. 

Well, with every powerful tool come caveats. The unused_ok option is a
expert option and if people who have difficulties understanding what
they are doing use it and encounter problems then it begs the question
why expert users need to suffer the consequences of their inabilities. I
use this option often and it is warranted in the current environment in
which phenix goes through a lot of revisions, which break compatibility
with previous versions, but provide new/better functionality I'd like to
use. And yes, if you are doing a couple of structures a day, reediting
the parameter file(s) is a serious drag.

>Finally, I don't understand what the trouble is to run this command:
>phenix.refine --diff-params your_old_parameters.def >

It is NOT usable in a automation environment. Since phenix goes through
so many releases, which change the parameter file and bails by default
if the parameter file does not match the current version, automation is
difficult to achieve. Correct me if I am wrong, but I believe it would
almost be impossible to pick up a previous refinement done with a old
phenix version again via an automated approach if the parameter file has
changed and phenix bails. Granted I could freeze the phenix version used
for automation and could maintain a couple of different versions for
different purposes, but that quickly becomes impractical. 

So in essence, for the "high-throughput-bleeding-edge-junky-users" the
--unsed_ok option is essential and I hope that it remains.



More information about the phenixbb mailing list