I have full EM map of antigen-antibody complex, which is subjected to local refinement to study the interface between two after applying soft mask. I have build and fit coordinates in local refinement map but not in the full EM map.
- Can I submit full map without coordinates and local refined map with coordinates
- If no, is it necessary to build and fit coordinates in full map as well?
- Or can I submit only local refined map with coordinates, because that completes our story?
What are the requirements for submission, because PDB has an option to submit experimental data without coordinates.
Any suggestion based on experience?
Thanks in advance!
It’s up to you - there’s no external check on the scientific content of your submissions, or between different submissions. (There is validation of the accuracy of the submitted coordinates and maps, but ultimately these are just suggestions, you are the final arbiter of what you deposit).
The full map is required to understand the quality of the data and the basis for obtaining the local refinement, so I strongly encourage you to at least deposit the full map without coordinates (but with its half maps, masks, etc). Those following your work need to be able to see what you have chosen to mask in the whole structure.
IMO you should ideally also submit coordinates with the full map, as it makes it easier to analyze the structures and create alignments, but if the antigen is well-characterized structurally (lots of apo and complex structures already in PDB), then it’s not absolutely necessary.