[phenixbb] Feature request: multi-stage refinement protocols from the GUI?

Tristan Croll tristan.croll at qut.edu.au
Mon Feb 22 06:36:54 PST 2016

Hi all,

I'm personally a big fan of the Phenix GUI, in particular for its automated record keeping for different runs. One thing I really wish it had, though, is the option to define more complex refinement scenarios as a single run. An example of what I'm talking about is the following protocol that has been working very well for me on a 3.6 Å strucutre:

- ~6 rounds of refinement of TLS, a single group B-factor and occupancies (the latter for a very small set of residues, mostly low-occupancy lead ions) with positions fixed

- ~8 rounds of TLS and individual B-factor refinement, still with positions fixed and with no further occupancy refinement

- ~8 rounds of TLS, B-factor and position refinement with torsion-angle restraints to the starting model

- ~8 rounds of position refinement with no restraints other than standard stereochemistry and metal bonds.

I know that all of this could be scripted quite easily from the command line, but it would be fantastic to be able to queue up such a protocol as a single continuous job in the GUI.

Best regards,


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