Hi Paul, Thanks so much for the quick response. Using the cifs from the new CCPEM library did the trick. Cifs from Phenix or an older version of CCP4 failed. I am not sure why (is there a flag in the cifs to tell Coot whether the molecule is a polymer or individual units?)
For others who may also face this issue: Cifs files from Phenix and Coot use different atom names in the SGN and IDS units. The chain I copied from 3IRI works with Phenix (after running phenix.ready_set and phenix_reduce), but not with the Coot Cifs. 1HPN works with Coot perfectly when the new CCPEM Cifs were imported. However, Phenix doesn't recognize it, only it worked when the CCPEM cifs were included in the inputs. Two related questions, can we (1) add disaccharide units to the existing chain?; (2) Delete monomers from the existing chain (I tried it, Coot removed the last monomer, but also the oxygen atom linking the last and the second to the last unit, which should remain and become a OH group)? Thanks again, Xuewu On Wed, Nov 1, 2023 at 12:22 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > On 01/11/2023 16:34, Xuewu Zhang wrote: > > > > Dear Paul, > > Can Coot handle heparin chains (not attached to protein) now? I was > > able to read a heparin chain in the PDB format, and import the cif > > restraints for the two sugar units (named IDS and SGN, from the phenix > > monomer library; Coot would recognize the molecule without them). > > However, it appears that the bonds between the sugar units are not > > recognized by Coot, and the units were pushed apart whenever I tried > > to do realspace refinement or regularize zone. I am not sure how to > > fix this, is there a way to tell Coot these units belong to a polymer > > and should be linked together? > > > > Dear Xuewu, > > > I used PDB code 1hpn as and example. > > I used the monomer library that comes with CCP4 and Coot. > > I selected one of the models (MODEL 1). > > I chose regularize fragment. > > Everything is connected as it should be and I could yank stuff around [1]. > > How can I reproduce what you are seeing? > > Regards, > > Paul. > > > [1] this is the technical term. > > > ######################################################################## > > 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/ > ######################################################################## 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/
