[chimerax-users] ligand not showing up

[Eric Pettersen]

Hi Eddie,
	Since some hexadecimal numbers are indistinguishable from decimal numbers despite representing very different values, ChimeraX does not support hexadecimal numbering for atoms past 99,999.  It supports Hybrid-36 numbering (which Greg mentioned) and "Amber" numbering, both of which are described briefly in the documentation of the serialNumbering keyword in the PDB section of the save command <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>.  You would have to use one of those numberings.  Alternatively you could change all the > 99,999 numbers to 99999 and I think that will work, though ChimeraX will complain bitterly about duplicate atom serial numbers.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 4, 2022, at 2:14 PM, Dr. Eddie via ChimeraX-users <chimerax-users at cgl.ucsf.edu> 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 <mailto: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 <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 <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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