[chimerax-users] ligand not showing up

[Dr. Eddie]

Thank you both! This makes sense. It seems I'll need to build off the lbl
script to write a converter. I appreciate the explanation!
Eddie

On Tue, Oct 4, 2022 at 5:00 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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> 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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-- 
Eddie
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