I have a protein of 106 residues (numbered from 1 to 106). I ran relax and cluster the resulting 200 poses.
cluster.linuxgccrelease -in:file:silent mysilentfile
But I got tons of such warning:
core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 111 requested but only 106 protein CA atoms found.
Why does cluster thinks I have 111 residues? Can I still trust the cluster result with all the warnings? Does this have anything to do with the "jump" concept?