How can I do a refinement only with the non-polar hydrogen atoms being removed?
Thanks!
If you want to use the server for that, you should first run a regular refinement, then save the json file and edit it to change the value of “delenph” to false.
Then submit that json file in the file upload interface.
Alternatively following the instruction from:
https://www.bonvinlab.org/software/haddock2.4/tips/advanced_refinement/
to set up a refinement run “manually” and define to keep the hydrogens.
Needs guru access to the portal.