Thank you all for your responses. I was confused after open file in coot and did some regid refinements. That file was saved, after this what I understood I can use this file for phenix real space refinements right or without doing in coot can do directly?. Can any suggest me my fit doesn't look like a 100% what should I could do for this. Thank you so much and happy holidays to all!!
On Wed, 18 Dec 2024, 16:14 Krieger, James M, < 0000e8decb6aa234-dmarc-requ...@jiscmail.ac.uk> wrote: > 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/ > ######################################################################## 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/
