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

Tristan Croll tristan.croll at qut.edu.au
Mon Feb 22 07:57:08 PST 2016

I know that feeling all too well!



From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Pavel Afonine <pafonine at lbl.gov>
Sent: Tuesday, 23 February 2016 1:47 AM
To: phenixbb at phenix-online.org
Subject: Re: [phenixbb] Feature request: multi-stage refinement protocols from the GUI?

Hi Tristan,

I've been willing to do this for years now. In fact it would help to automate refinement by dynamically casting refinement strategies and parameters as refinement progresses.

Unfortunately no, this functionality is not available. It is not too difficult to implement, may be a week of focused work. The biggest problem is that the (only) way this can be done will brake a lot of backwards compatibility and will require a lot of changes in the GUI because the main{} scope of parameters will have to become of type "multiple". So far this was the major demotivator for me to do it.

All the best,

On 2/22/16 15:36, Tristan Croll wrote:

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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