One may need to set a preference in Coot to allow such a situation to be viewed. Paul helped me but I can't find the email.
Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Wed, Feb 15, 2023 at 12:37 PM Eleanor Dodson < 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > I thought that REFMAC tolerated dual occupancies if the sum of the two > conformers was <= 1.0? > Eleanor > Will test.. > > On Wed, 15 Feb 2023 at 16:37, Stuart McQuarrie < > 0000974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote: > >> I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some >> refinement have noticed partial occupancy of it's hydrolysed form 2x A3, >> which has a cyclic 2'-3' phosphate on the terminal ribose. >> >> I tried fitting both ligands with 50% occupancy, but refinement doesn't >> allow them to occupy the same space. >> >> I subsequently tried text editing the pdb file, adding altloc identifiers >> to the ca6 and the 2 A3 molecules, making sure they were same chain and >> residue number as per this ccp4bb archive: >> http://www.phenix-online.org/pipermail/phenixbb/2011-March/016768.html. >> However, before I refined I checked in coot and all the ligand atoms are >> scattered and disconnected. >> >> I have thought about using coot to generate an alt conformation of ca6 >> and then text editing the B conformation to be split and have a 2'-3' >> cyclic phosphate. I am not sure if this is the correct way because it is a >> different chemical structure, so I could use some advice. >> >> Kind regards, >> Stuart >> >> ######################################################################## >> >> 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/
