> Hello, > > > > I’m using the Coot 0.9.8.91 EL. I am working jointly with a computational > team who are doing simulations on our PDB model. I’ve added hydrogens to > my model using Coot’s Validate -> Probe clashes function. The computational > team asks, when COOT adds protons using the probe clashes function, how > does it assign protonation states to residues? Is it using something > sophisticated that we can trust for our computational simulations or should > the computational scientists use their own methods for determining > protonation states?
Coot uses (in this case) the programme/method reduce from the Richardson lab to add hydrogens. You will find more information on reduce here: http://kinemage.biochem.duke.edu/software/reduce/ HTH, B > > Thank you for your time answering this question, much appreciated! > > > > Best, > > ‘Kate’ Sun Kyung Kim > > > ________________________________ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fww > w.jiscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C02%7CBernhard.Lohk > amp%40KI.SE%7C72deacec99e34d17ea2d08dc212b7cbb%7Cbff7eef1cf4b4f3 > 2be3da1dda043c05d%7C0%7C0%7C638421718169055485%7CUnknown%7CT > WFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ > XVCI6Mn0%3D%7C0%7C%7C%7C&sdata=uonT4Uc19QH6B7M2PiSaPmmOwa > dhK3ITmwZu7mzwcXs%3D&reserved=0> *************************************************** 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 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/medarbetare/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://ki.se/en/staff/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/
