[chimerax-users] ligand not showing up

[Greg Couch]

Hex numbers don't work for atom serial numbers.  You'll need to use the 
hybrid-36 format.  That is a base 36 format where the capital letters 
are additional digits.  See https://cci.lbl.gov/hybrid_36/.

You should also consider switching to the mmCIF format, which does not 
have a limit on the number of atoms.

     -- Greg

On 10/4/22 14:14, Dr. Eddie wrote:
> 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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