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 >>> >> >
