I am trying to do model a loop using loopmodeling mode and want to keep the rest structure rigid. when I run loopmodel.linuxgccrelease. A lot of WARNING lines like
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 17
in file . Best match rsd_type.
core.io.pdb.file_data: [ WARNING ] discarding 9 atoms at position 30 in file . Best match rsd_type
I found that some positions in other regions were changed after loop modeling.
I tried -loops:natsc and -loop:refine_only. seems both changes the side chains