The thresholds Coot uses for the different colours in the dialogue are: < 0.0 Black < 1.4 Green < 2.2 Yellow < 3.0 Orange >= 3.0 Red
On Mon, 20 May 2019 at 09:48, Ahmad Khalifa <underoath...@gmail.com> wrote: > That's great, thanks. What are the cutoffs that coot uses? I want to use > Coot native parameters first to do some testing before I do any major > modifications. > > Regards. > > > > On Mon, May 20, 2019 at 4:12 AM Paul Bond < > 000030b0cd59fccb-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Hi Ahmad, >> >> If you want to use the values from the accept refinement dialog, they are >> available from the refine_residues function: >> >> imol = 0 >> residue_list = [["A", 10, ""], ["A", 20, ""], ["A", 30, ""], ["A", 40, >> ""]] # for example >> >> set_undo_molecule(imol) >> for rs in residue_list: >> rnr = residues_near_residue(imol, rs, 4.2) >> rset = rnr + [rs] >> with AutoAccept(): >> stat_summary = refine_residues(imol, rset) >> if stats_are_acceptable(stat_summary): >> pass >> else: >> apply_undo() >> >> You will still need to write the stats_are_acceptable function with your >> own cutoff values. >> >> Kind regards, >> Paul >> >> On Mon, 20 May 2019 at 02:30, Ahmad Khalifa <underoath...@gmail.com> >> wrote: >> >>> But that function should already be implemented in the green flags that >>> I get in the accept refinement dialog, no? >>> >>> On Sun, May 19, 2019, 7:19 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> >>> wrote: >>> >>>> On 19/05/2019 21:40, Ahmad Khalifa wrote: >>>> > Hello, >>>> > >>>> > I want to write a script that does the following: >>>> > >>>> > for a bunch of chains and atom numbers: >>>> > go to chain letter and atom number >>>> > do sphere refinement >>>> >>>> This should get you started: >>>> >>>> imol = 0 >>>> residue_list = [["A", 10, ""], ["A", 20, ""], ["A", 30, ""], ["A", 40, >>>> ""]] # for example >>>> >>>> set_undo_molecule(imol) >>>> for rs in residue_list: >>>> rnr = residues_near_residue(imol, rs, 4.2) >>>> rset = rnr + rs >>>> distortion_pre = residues_distortions_py(imol, rset) >>>> with_auto_accept([refine_residues, imol, rset]) >>>> distortion_post = residues_distortions_py(imol, rset) >>>> if post_model_is_better_model(distortion_pre, distortion_post): >>>> pass >>>> else: >>>> apply_undo() >>>> >>>> Have fun writing the post_model_is_better_model() function >>>> >>>> Paul. >>>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the COOT list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 >>> >> >> ------------------------------ >> >> To unsubscribe from the COOT list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 >> > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
