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
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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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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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
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@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 >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users@cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users@cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >
-- Eddie
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@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@cgl.ucsf.edu <mailto: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... <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 <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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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@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@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@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Eddie
participants (3)
-
Dr. Eddie -
Eric Pettersen -
Greg Couch