Ccg-chemistry-faq/Protein Structure Import Problems
WebMO may not properly import your molecule from a .pdb file, depending on how the .pdb was created. For example, for NMR structure determination, sometimes hydrogens are not listed as H but as Q (for reasons we need not get into here). Although visualization programs like PyMOL will work fine, WebMO's import feature doesn't like this very much.
If your file looks like this, you're OK:
However, if your file looks more like this:
you'll need to make several corrections before proceeding.
1) Replace any Qs, as circled above, with H.
2) Delete any numbers PRECEEDING an H (any annotation afterwards, like HAX, is fine).
This should solve basic import problems.