Hi Yong, Keep the numbering continuous during the coot and Refmac cycles of building and refinement. Refmac will have trouble keeping your model within the electron density map with a break in the chain. So, for now, keep the numbering continuous. Once you are satisfied with your model and ready to present/deposit, use the "Renumber Residues" in Coot to renumber the residues to their original numbering.
Hope this helps! Gyan On Fri, Jul 24, 2020 at 8:42 AM Yong Tang <[email protected]> wrote: > Dear all, I have a loop truncation that could be explained as > ProteinName(1-20)-GSSGSS-(40-500), where residues 21-39 was replaced with a > GSSGSS linker. Now the problem is in Coot, how do I define this mutant in a > way that I could still preserve the numbering of the native residues while > allowing the loop to become an integral part of the continuous polypeptide > chain? > > A related question is then would Refmac handle such a model properly in > refinement? > > Thank you in advance for your help, -yong > > ------------------------------ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > -- Gyanendra Kumar https://www.linkedin.com/in/gyanendrakumar https://scholar.google.com/gyanendrakumar <https://scholar.google.com/citations?user=lnil0IQAAAAJ&hl=en> ------------------------------------------------------- ######################################################################## 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/
