I guess you mean that you’ve done an initial global rigid body fit and you still want to do some refinement to get better local fits?
Refmac servalcat is a good option and uses two half maps in MRC format. It comes as part of ccpem but does require ccp4 to be installed too Or alternatively, you could use phenix, which has a real space refinement option for cryo-EM. Best wishes James > On 18 Dec 2024, at 21:04, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > On 18/12/2024 18:17, tim smith wrote: >> Hi all, >> >> Can you please advise once we fit the map and open in coot. What is next >> step to do in coot. > > I am somewhat confused. Once you have done the fitting then you're done. > Right? You can run your model through (another) refinement program before you > analyse and deposit - servalcat springs to mind. > >> I tried refmac but that required ccp4 file which doesn't have. > > Refmac is part of the CCP4 Suite. You need CCP4 to get Refmac. > > One can build Servalcat from source - https://github.com/keitaroyam/servalcat > - and that doesn't need CCP4 - however I doubt that is easy for "newbies." > >> Please some one can help in elaborating and sharing any tutorial would be >> helpful. I'm new bie and first time I am trying model building. > > There are some cryo-EM tutorial on my blog: > > https://pemsley.github.io/coot/blog/ > > e..g this one: > > https://pemsley.github.io/coot/blog/2022/08/27/Coot-Cryo-EM-Tutorial-Part-1.html > > There are some tutorials on YouTube (e.g. sbgrid) I should make more. > > Paul > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
