Along the same lines as Dialing’s recent post about inserting a residue, I’d like to ask: Is it possible to insert a residue with an insertion code in the residue number? For example, what’s the best way to insert residue 100A between residues 100 and 101?
This situation arises frequently for me in antibody CDR loops, for example. I ran into it most recently just last week, and Coot wouldn’t allow this kind of insertion, even though the consecutively numbered residues were too far apart to be covalently linked. (In the terminal window, it explained "that residue was not at a terminus.”) My workaround has been either to increment the residue numbers of the C-terminal portion of the chain, then renumber manually in a text editor; or, to position a lone amino acid in approximately the right spot, save the coordinates, copy them manually into the working PDB and adjust the numbering in a text editor, reload the PDB in Coot, and real space refine the loop with the insertion. Any suggestions for how to do this more efficiently? Thanks! Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jan 14, 2015, at 9:54 AM, Emilia C. Arturo (Emily) <ec...@drexel.edu<mailto:ec...@drexel.edu>> wrote: If the residues are consecutively numbered (Calculate > Renumber residues), and are assigned the same chain ID (Calculate > Change Chain ID), Coot might surprise you and link them on its own. On Wed, Jan 14, 2015 at 9:39 AM, Zhijie Li <zhijie...@utoronto.ca<mailto:zhijie...@utoronto.ca>> wrote: Have you done it? 1) Click “add residue...” 2) Click that “real space refine zone” button. You will see what will happen. From: Dialing Pretty<mailto:000003f1d08ed29c-dmarc-requ...@jiscmail.ac.uk> Sent: Wednesday, January 14, 2015 9:24 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal Dear All, Suppose I delete a residue ( residue 100 for example) for outlier refinement, then I add the same residue at the C-terminal of residue 99 (by Add terminal residue function of the Coot). By coot, how can I connect the C-terminal of residue 100 to the N-terminal of residue 101? I am looking forward to getting your reply. DIaling
