Hi, I have a following problem in dev-874 version: 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. 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. Has this been solved in latest builds perhaps? Thank you, Leo -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915
On Thu, Mar 15, 2012 at 12:29 PM, Leonid Sazanov
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 hope. -Nat
Hi, I downloaded dev-1005 version and in Graphics window there is no Sec.Str.? Thanks, Leo
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. Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915 On 15/03/2012 19:29, Leonid Sazanov wrote:
Hi, I have a following problem in dev-874 version:
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. 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. Has this been solved in latest builds perhaps? Thank you, Leo
On Mon, Mar 19, 2012 at 1:47 PM, Leonid Sazanov
I downloaded dev-1005 version and in Graphics window there is no Sec.Str.?
This is probably because you're using Linux, where the toolbar buttons hog more space than on Mac and the relevant button is probably being pushed off the right edge of the toolbar. Try maximizing the window and see if that helps. (Sorry, the GUI toolkit won't let me set the font size on these from Python - I will see if there's another way.) By the way, I'd recommend trying dev-1008 instead - I made a few other minor changes that may be helpful for your situation. -Nat
participants (2)
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Leonid Sazanov -
Nathaniel Echols