Hi all, Can someone please help us out with forming a PTM to a side chain? We can refine the PTM ligand in its density (as a non-bonded ligand), but the side chain will not stay within the distant specified on the PDB file. So far, we tried: 1. Using "make link" in Coot, between the specific atoms (side chain and PTM) 2. Made sure the line is present in the pdb file: LINK NZ LYS A 630 C11 PTM A 701 1555 1555 1.33 [PTM is an acronym for our specific PTM. I'm keeping it anonymous for now, but the modification is on a Lys] 3. Generated a PTM.cif file for the ligand using eLbow, and included it in real time refinement (it's an EM map) in Phenix
We also tried to use Isolde (sorry...) and force "bond sel reasonable false" followed by an Isolde run. But then Isolde, which could recognize this specific PTM, insisted on adding extra incorrect hydrogens (ie Lys Nz has *2H* (instead of 1) plus the connection to CE, plus the connection to the PTM). We manually removed the extra hydrogens before another round in Phenx, but the bond between the Nz and the PTM still break the laws of chemistry (we get sharp angles, for example). We saw people depositing those structures, and it seems fine in theirs (reasonable bond length and angle) Can anyone have other suggestions, please? Thanks for your help ######################################################################## 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/
