Hi Stuart, the answer, I think, is here: https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12 Pavel
On Wed, Feb 15, 2023 at 8:37 AM 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 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/
