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@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.ht... 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