I want to show certain atoms in the main chain, but ribbonjr hides all main chain atoms as part of the ribbon. How can I show them?
It can’t be done directly; you have to resort to dirty tricks. However, the “dirty trick” isn’t hard to pull off. Essentially, you save a file containing just the main chain atoms you want shown to a new file, then open the new file in Midas along with the original file and display them both in ribbonjr. The procedure is as follows: • Use the standard Midas display commands (e.g. display, show) to show only those main chain atoms you want shown with the ribbon. • Save them to a file using pdbrun: pdbrun nouser cat > filename • Edit the file to change the atom names so that they are no longer the names of main chain atoms (e.g. “CA” to “CX” or “N ” to “NX”). Remember to keep all other columns aligned. • Read the edited file back into Midas, aligned as it was originally, with: open original filename • Display both the original and new files as you want them to look, and run ribbonjr.
