Fantom atom when selecting a missing residue

[chmnk]

In pymol-open-source 2.5 and 3.0, when I load the 1c1v PDB file and try to select a missing residue,

fetch 1c1v
select ch_r150, chain H and resi 150

I get a 1-atom selection, and that atom does not have coordinates. Is it done like that by design?

[JarrettSJohnson]

Depends on the file that PyMOL parses the structure data from. From the 1c1v .cif file, there is a residue provided by the structure file at residue position 150, and I assume we just insert a "non-physical" atom there that lacks coordinates. For the 1c1v .pdb file, the missing residues are skipped.

[speleo3]

You could remove those atoms which don't have coordinates by:

remove not present

Before: After:

[chmnk]

@JarrettSJohnson @speleo3 thank you!