[chimerax-users] ligand not showing up

[Dr. Eddie]

Thank you! It seems the error occurs at the 100000 atom. The numbers there
start to be hexidecimal. It starts to see the numbers in base 10 and
hexidecimal numbers as the same so it counts them as duplicates (like 18700
in decimal and 18700 = 100096 (decimal)). Is there some conversion I need
to do?
Thanks!
Eddie

On Tue, Oct 4, 2022 at 4:01 PM Greg Couch <gregc at cgl.ucsf.edu> wrote:

> Sorry, that was only one of the problems.  As you can see from the log,
> when you open your file in ChimeraX, there are many bad PDB records.
> See
>
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html
> for details about the format, or the full PDB format documentation at
> https://www.wwpdb.org/documentation/file-format.  There are also lots of
> duplicate atom serial numbers that confuse things.
>
>      -- Greg
>
> On 10/4/22 13:52, Greg Couch via ChimeraX-users wrote:
> > The coordinates are in the wrong columns for your HETATM residues.
> > Remove the spaces after HETATM.
> >
> >     -- Greg
> >
> > On 10/4/22 13:19, Dr. Eddie via ChimeraX-users wrote:
> >> Hi all,
> >> I've got a pdb and I can't seem to get ChimeraX to recognize the
> >> ligand (resname STR) at the end of the pdb. I've modified the ATOM to
> >> be HETATM but it still does not show up. I hide solvent and the
> >> lipids and I know where it should be (from seeing it in vmd) but only
> >> a void is there. Any ideas what is wrong with the pdb?
> >> Thanks,
> >> Eddie
> >>
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>


-- 
Eddie
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