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/
