How to visualize structures

[OYH-2024]

/mnt/e/rosetta/rosetta.binary.ubuntu.release-371/main/source/bin/extract_pdbs.linuxgccrelease -gen_potential -overwrite -beta_cart -in:file:extra_res_fa clusters_CA_cluster_centroids_0_290.params -in:file:silent E3L_6DO3_0_0.out -in:file:tagfile 1.tag -missing_density_to_jump -in:file:fullatom
I tried to visualize the structure using this command, but the structure of the small molecule is completely distorted