Sorry, this is my fault. The Coot extension in Phenix has this line near the beginning:
set_do_probe_dots_post_refine(1) which ensures that the dots will be refreshed after you make changes - but if you didn't want the dots in the first place, it's less helpful. I'll disable this until I figure out a smarter solution. (There will be a new Phenix release next week with this change - or the next nightly build.) However, the interaction between the generic display object control panel and the post-refinement update in Coot sounds like an independent bug, since it's overriding your display settings. - other Nat On Fri, Apr 11, 2014 at 11:22 AM, nathanielclar5 . <[email protected] > wrote: > A delayed update... > > Can you explain that last comment further? How I can turn 'Interactive > dots' on? I think that might solve my problem. > > I figured out how to turn the dots off with 'Show probe dots in coot' > they go away, but after using refinement, or rotate/translate, they > reappear. Even if I turn off the dots, then disconnect the window from > Phenix, they reappear after any model manipulation. The generic display > object now works. I can turn the dots off within coot using the 'generic > display objects', but, new generic display objects appear after every > manipulation of the model. It's awash, I still have to actively turn off > the dots constantly, either with phenix 'show probe dots in coot' or with > coot 'generic object display'. > > Any suggestions? Should I just take the practical solution of opening > stand-alone coot sessions? > Thanks, > Nat > (using phenix 1.9 pre-1669 and coot 8-pre 5001) > > > On Thu, Jan 31, 2013 at 1:19 AM, "ing. Jan Stránský" > <[email protected]>wrote: > >> Also turning "Interactive dots" on in coot could help. It overrides any >> other molprobity dots when you run real space refinement, choosing >> different rotamer or editing chi-angels for example. >> Cheers, >> Jan >> >> >> On 01/30/2013 09:34 PM, Nathaniel Clark wrote: >> >>> I get the same result when I select Draw->generic display >>> objects-nothing at all happens (not even a window hidden behind the >>> main coot window). >>> >>> I think I stumbled on the solution though, if I go to the molprobity >>> tab in Phenix, I can toggle the dots on or off in coot! >>> Nat >>> I guess I will have to just close out the Phenix-initiated coot window >>> and start a fresh one. >>> >>> On Tue, Jan 29, 2013 at 3:19 PM, Nat Echols <[email protected]> >>> wrote: >>> >>>> On Tue, Jan 29, 2013 at 12:33 PM, Nathaniel Clark >>>> <[email protected]> wrote: >>>> >>>>> When I use a coot window that was started by Phenix, it shows those >>>>> 'molprobity' dots which represent the Van Der Waals surface. Can >>>>> anyone tell me how to turn those off? >>>>> >>>> In theory, Draw menu --> Generic Display Objects... has the toggles >>>> for these, although for some strange reason it does nothing on the >>>> version I have installed here, which I believe came from the CCP4 home >>>> page. (Nor does opening the Python scripting console and typing >>>> "generic_objects_gui()".) >>>> >>>> I will add an option to Phenix to disable the automatic display, in any >>>> case. >>>> >>>> - the other Nat >>>> >>> >> >
