Failed to add residue HME at position 209 to surface - cannot find radius for FE1

[black-desk]

When my molecule includes a metal atom (FE1) with 2-letter atomtype, Rosetta produces the following error:

core.scoring.sc.MolecularSurfaceCalculator: [ ERROR ] Failed to add residue HME at position 209 to surface - cannot find radius for FE1

I tried resolving this by adding a line like * FE* 1.41 to the sc_radii.lib file, but the error persists.

Root Cause Analysis

After investigating the relevant code:

rosetta/source/src/core/scoring/sc/MolecularSurfaceCalculator.cc

Lines 325 to 330 in 695b0f2

	strncpy(scatom.atom, residue.atom_name(i).c_str()+1, sizeof(scatom.atom)-1);
	if ( !AssignAtomRadius(scatom) ) {
	TR.Error << "Failed to add residue " << residue.name3() << " at position " << residue.seqpos() << " to surface - cannot find radius for " << residue.atom_name(i) << std::endl;
	return 0;
	}

I believe the issue occurs when copying residue.atom_name(i) to scatom.atom, as the code skips the first character. However, when generating the error message, it prints the full residue.atom_name(i), which is misleading.

Workaround

Instead of adding * FE* 1.41 to sc_radii.lib, adding * E* 1.41 works correctly. This confirms that the code is looking for the atom name without the first character.

[roccomoretti]

Note that the default radii for the MolecularSurfaceCalculator are really only intended for use with protein-only structures. For general usage which includes non-protein or non-canonical residues, you may want to enable the use_rosetta_radii setting on MolecularSurfaceCalculator::settings -- I believe most end-user usage of MolecularSurfaceCalculator has this as an option.