* Why not rename chains and if necessary renumber
Sure, that is how I had to do it. But with many chain fragments and residues in the high thousands and medium to low resolution this becomes cumbersome. Many domain/motif/helix connections are initially exploratory and determine the residue numbers/sequence based on side chain fit. Then everything changes again when you correct. I don’t think anything is unrealistic about the link per se – the chain assignment or residue numbers are unrealistic in the beginning. Best, BR From: Mailing list for users of COOT Crystallographic Software <[email protected]> On Behalf Of Eleanor Dodson Sent: Wednesday, March 31, 2021 23:43 To: [email protected] Subject: Re: Link residues in different chains Why not rename chains and if necessary renumber residues to make a sensible single chain? Very easy with the edit options and much simpler than creating an unrealistic link?? I find myself going that often after an build molecule run. Eleanor On Thu, 1 Apr 2021 at 00:40, Paul Emsley <[email protected] <mailto:[email protected]> > wrote: On Wed, 2021-03-31 at 16:34 -0700, Kevin Jude wrote: > Just want to note that it's not that esoteric - it's not uncommon to > find (or engineer) disulfide bonds between chains, eg 6WDQ, 6BJ8, and > others that I have worked on. Being able to RSR those links would be > quite useful! > > -- > Kevin Jude, PhD (he/him/his) > Structural Biology Research Specialist, Garcia Lab > Howard Hughes Medical Institute > Stanford University School of Medicine > Beckman B177, 279 Campus Drive, Stanford CA 94305 > Phone: (650) 723-6431 > > > On Wed, Mar 31, 2021 at 3:04 PM Paul Emsley < > [email protected] <mailto:[email protected]> > wrote: > > On 31/03/2021 22:08, Bernhard Rupp wrote: > > > > > > I spectacularly fail trying to link for real space refine 2 > > different chains with the modelling/make link > > > command. > > > > The bonding in Coot's RSR only works within the chain - including > > links. (You can make links between chains, > > but RSR won't use them.) > > > > > How can I do that short of renaming my chains? > > > > If I understand what you are trying to do (sounds a bit esoteric) > > then I don't think that there is a way. > > > > Paul. > > OK, interesting. I've made a note. Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1> &A=1 This message was issued to members of www.jiscmail.ac.uk/COOT <http://www.jiscmail.ac.uk/COOT> , a mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk> , terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ _____ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1> &A=1 ######################################################################## 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/
