[PyMOL] Bond Editing

Hi all,

This is a long shot. But I am having problems fitting a model to a cryoEM map with bond modifications completed in pymol and I am hoping someone can help.

I downloaded a structure from the PDB database, and I am adding two bonds between nucleotides. However, these bonds do not appear to save correctly to mmCIF or PDB, often being lost as they do not show up in ChimeraX. When trying to open these files again in pymol, I can see random things like a hydrogen with two bonds in place of the new bond I made. The modifications appear to save okay to mol2, but phenix refuses to use the file afterwards anyway.

I feel like I am missing a step because phenix asks for restraints and when I try to run elbow, it just crashes with the PDB and mmCIF files. The Mol2 file does not load in phenix and just crashes phenix. I have gotten the mol2 file to open in chimeraX and then save as pdb afterwards. I did generate restraints for this file, but it completed this without the actual modifications I made so was pointless.

So, I am kind of stumped right now. Has anyone had any experience with creating new bonds in PDB files and saving them for use with fitting to cryoEM maps and refinement?

Thanks,
Jason Woodgate
Newcastle University.