Agreed with regards to the dots. Actually it would be really nice if these were separate from the probe clash dots obtained when running probe on the whole molecule. Right now when I adjust rotamers and have the probe dots active the dots from the probe clashes analyses are overwritten.
-----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Oliver Clarke Sent: Wednesday, October 28, 2015 1:12 PM To: COOT@JISCMAIL.AC.UK Subject: Re: [COOT] no clash display in realtime refine within COOT Also, relating to set_do_probe_dots_on_rotamers_and_chis - it would be better I think if probe dots were dismissed upon dismissing the rotamers dialog. Right now they remain, even if the rotamer they relate to was not selected. (Also, the latest nightlies still give a segfault upon launch when built on Mac - any chance of a fix?) Incidentally relating to rotamers, I would love to have a shortcut to cycle through possible rotamers for the active residue without having to launch the rotamers dialog, but I can't seem to figure out how to build that using any of the python functions that are available - anyone have any ideas? Oli. On Wed, 28 Oct 2015 14:11:40 +0000, Schubert, Carsten [JRDUS] <cschu...@its.jnj.com> wrote: >May be worthwhile to check if these settings are in effect (snipped >from my coot.py) set_find_hydrogen_torsion (1) >set_do_probe_dots_on_rotamers_and_chis (1) >set_do_probe_dots_post_refine (1) > >HTH > > Carsten > >-----Original Message----- >From: Mailing list for users of COOT Crystallographic Software >[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Paul Emsley >Sent: Tuesday, October 27, 2015 10:55 PM >To: COOT@JISCMAIL.AC.UK >Subject: Re: [COOT] no clash display in realtime refine within COOT > >On 25/11/2014 20:45, 李智海 wrote: >> Hello, >> I have met a problem when I performed real-space refine handling with >> COOT software from Phenix. It did not show the surrounding clashes of >> the refined atoms so that I can not see whether the refining is >> appropriate. The tool Probe-clashed in Validate works fine, but it >> shows the global clashes of the whole molecule and it’s not realtime. >> > >It used to be the case that Coot updated the local probe dots locally after a >(Coot) refinement. I have not tried this in a long time however and never with >the Phenix interface. > >I will make a note to review this. > >Paul.
