Hi Pascal, You don’t say which Coot version you are using? There is a minor difference. Either way the pythonic sphere_refine function takes an argument radius which can be changed, so (for radius 2.5):
Coot 0.9.x: sphere_refine(2.5) Coot 1.x import coot_fitting coot_fitting.sphere_refine(2.5) Note, the build in function rsr_sphere_refine has a fix radius (maybe it shouldn’t...). HTH, B *************************************************** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Teaching Unit/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 [email protected] | ki.se > -----Original Message----- > From: Mailing list for users of COOT Crystallographic Software > <[email protected]> On Behalf Of Auffinger Pascal > Sent: 28 May 2025 21:58 > To: [email protected] > Subject: using sphere_refine with distance restraints > > Hi, > > I would like to do a sphere_refine around an ion in my scripts. > I would like to select the closest residues - say at less than 2.5 Å of the > ion. > > The command is sphere_refine() > The default radius is 3.5 Å - can this radius be modified to 2.5 Å ? > > What are the arguments of sphere_radius() ? > Is it possible to use something as "residues_near_position" > > Then, I would like to use distance restraints like for example restraining the > distances of the six coordinated Mg2+ atoms to 2.07 angs. > > Any thoughts ? > > Thanks > > Pascal > > ################################################################ > ######## > > To unsubscribe from the COOT list, click the following link: > https://www/. > jiscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C02%7CBernhard.Lohk > amp%40KI.SE%7C2f2f859a9b394c96ed2508dd9e2208d2%7Cbff7eef1cf4b4f32 > be3da1dda043c05d%7C0%7C0%7C638840591351661956%7CUnknown%7CT > WFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXa > W4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=h5G > OMnGmySJOopwMsYF6y29D4YEIYBM0UrPsKkKTi28%3D&reserved=0 > > This message was issued to members of > http://www.ji/ > scmail.ac.uk%2FCOOT&data=05%7C02%7CBernhard.Lohkamp%40KI.SE%7C2f > 2f859a9b394c96ed2508dd9e2208d2%7Cbff7eef1cf4b4f32be3da1dda043c05d > %7C0%7C0%7C638840591351684387%7CUnknown%7CTWFpbGZsb3d8eyJFb > XB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTW > FpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=owSqxLnJqoaSL9eJ3ZU4 > D6De%2BpZpCVC97x3B6zOW5Tw%3D&reserved=0, a mailing list hosted by > http://www.ji/ > scmail.ac.uk%2F&data=05%7C02%7CBernhard.Lohkamp%40KI.SE%7C2f2f859 > a9b394c96ed2508dd9e2208d2%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0 > %7C0%7C638840591351698785%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0e > U1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCI > sIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=L3n6YVgUUjuKoVuHjs5AyAKQ > H%2BBR2z9jV4sblQ3Q0L0%3D&reserved=0, terms & conditions are available > at > https://www/. > jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7CBernhard.Lohka > mp%40KI.SE%7C2f2f859a9b394c96ed2508dd9e2208d2%7Cbff7eef1cf4b4f32b > e3da1dda043c05d%7C0%7C0%7C638840591351711009%7CUnknown%7CTW > FpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW > 4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=7RxTZC > ufJeMQND0lTT7pF50mazgzLS6vKkXNFTFdqec%3D&reserved=0 När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/om-ki/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://staff.ki.se/data-protection-policy>. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
