[phenixbb] GUI parameter files

Nathaniel Echols nechols at lbl.gov
Thu Mar 15 14:17:30 PDT 2012

On Thu, Mar 15, 2012 at 12:29 PM, Leonid Sazanov
<sazanov at mrc-mbu.cam.ac.uk> wrote:
> If I restore a previous job in refine GUI, to run it with modified settings,
> and include a new parameter file .eff with definitinon of secondary
> structure restrains, these new restrains are combined with previously used
> restrains.
> How do i get rid of previous restrains? Older file is not visible in inputs,
> but its settings are still used.

It's messy - click "Graphics" on the toolbar, then "Sec. Str." on the
toolbar of the graphics window, which will open the editor for these
restraints.  I will make this more accessible ASAP, and I'll add a
menu option to simply wipe out the current definitions.

> And in general, how can one be sure which parameters are used at the start
> of each refine run?
> If older settings loaded from .eff or .param file are not visible, the only
> way is to look through new .eff file, which takes a lot of time.

The "Edit parameters and run" option is the best solution, although
that does involve reading the .eff file.   Alternately, "View all
parameters" in the Settings menu will show you a tree version of this,
which may be easier to navigate.

> Has this been solved in latest builds perhaps?

Not exactly- the other custom geometry restraints are handled much
better now, but the problem you describe could still be an issue.
However, what it will now do is include the parameter files as actual
parameters, instead of merging them in.  This won't fix your current
problem but it will prevent it from happening again in the future, I


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