Hi, I have succesfully solved APO structure (chain A) with NOE data with ccpnmr and nih-xplor using the well written guide for structure solving provided by:
I had much less success with a protein-peptide complex with phosphoserine (SEP) however.
However, when I finished assigning the NOEs for the Holo structure, where there are two chains: A (protein) and B (peptide with phosphoserine SEP), the script.sh generated by ccpnmr works and runs to completion, but with unexpected outcomes. The script.sh deletes my phosphate atoms on my SEP molecule, and renames it to SER. The protein size quadrupled from 44 residues to 188 residues due to the program expecting symmetric dimers if the chain length is larger than 1, and replicating and stitching together my peptide and protein repeatedly.
Problem 1. Phosphoserine (SEP) is recognised by NIH-xplor and its protein topology / potential files, but the script.sh has many parts that forcefully converts SEP to SER instead. I have identified that the:
“from iupacNaming import toIUPAC, fromIUPAC” and
“toIUPAC()” code does not having SEP, and added in the SEP atom naming into iupacNaming.py in NIH-xplor/python but that does not fully fix things. The pdb generation script and talos also converts SEP to SER many times throughout the script.sh, and this causes the final stimulated annealing step to be off, as the SEP is key for binding, as SER is non-binding. This problem is most obvious at the fold.py step, and with the out.nef step, at which point the SEP is completely changed to SER.
Problem 2: The script.sh handles symmetric dimers in the workflow, but cannot handle hetero, non symmetric multimers. It automatically reads through the protein chain in the .nef file and treats chain A and chain B like a single chain very early on, despite it being stated that:
35 A 39 GLY middle . .
36 A 40 ASN middle . .
37 A 41 SER end . .
38 B 501 GLY start . .
39 B 502 LEU middle . .
The protein and peptide are distinct.
I have tried changing the code line by line, but it has taken me a long time without much success. Is there any way for the code to become more generalisable to handle SEP (already encoded in NIH-xplor) and avoid funny multimerisation issues?
Thank you.