Hi, You can save the rigid fit model w.r.t the density map in chimera, then load them in phenix to start real space refinement.
Regards Subhomoi On Thu, 19 Dec, 2024, 6:24 pm tim smith, <stim52...@gmail.com> wrote: > 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 > ######################################################################## 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/
