Hi all, First of all, I'm tickled (if also a little daunted) to learn that somebody's using ISOLDE as the basis of undergrad teaching assignments! I can confirm Kevin's advice that removing those extraneous spaces and TER lines gives you a model that loads correctly in ChimeraX. One other error in your file that may cause confusion (it did for me at first): Val C145 has a duplicated atom (see below). Delete that line (or simply deleting all hydrogens before running addH) and you should be mostly good to go. Best, Tristan ATOM 3838 CG2 VAL C 145 -34.057 -60.135 -41.432 1.00 54.54 C ATOM 3839 H VAL C 145 -31.042 -58.695 -40.969 1.00 77.79 H ATOM 3839 H VAL C 145 -31.042 -58.695 -40.969 1.00 77.79 H On Thu, May 14, 2026 at 11:29 PM Kevin M Jude via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Byron, pdb is a plaintext file and it has strict rules about what information goes in what column of the file. For example residue type must go in columns 18-20. You can google for more info on pdb format specifications if you like. But in your case, there is for some reason a misalignment at the cysteine atoms: ATOM 1324 CG2 VAL D 145 -1.412 -45.504 -39.926 1.00 63.63 C ATOM 1325 H VAL D 145 -4.587 -46.874 -39.579 1.00 68.04 H TER 5057 VAL D 145 HETATM 1326 N AKG D 146 -3.172 -48.663 -42.861 1.00 57.79 N HETATM 1327 C5 AKG D 146 -3.325 -49.926 -43.595 1.00 60.48 C HETATM 1328 C AKG D 146 -4.345 -50.910 -43.015 1.00 57.22 C HETATM 1329 O AKG D 146 -5.534 -50.795 -43.265 1.00 54.67 O HETATM 1330 C6 AKG D 146 -1.965 -50.574 -43.892 1.00 69.38 C HETATM 1331 H AKG D 146 -2.831 -47.883 -43.403 1.00 57.79 H HETATM 15 O3 AKG D 146 -1.290 -53.701 -43.091 1.00 20.00 O HETATM 16 C7 AKG D 146 -1.596 -53.313 -44.191 1.00 20.00 C HETATM 17 S1 AKG D 146 -1.629 -51.552 -44.626 1.00 20.00 S HETATM 18 C8 AKG D 146 -1.983 -54.139 -45.371 1.00 20.00 C HETATM 19 C9 AKG D 146 -3.234 -54.949 -45.065 1.00 20.00 C
You can open the file in any text editor (like textedit, nedit, vi, but not a word processor), delete the two extra spaces that come after the “HETATM” for those atoms, and everything should line up and be read properly. You should also delete the TER line that comes after Val 145, that indicates a chain termination.
hth
-- Kevin M. Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305
*From: *TheWildBynapie via ChimeraX-users <chimerax-users@cgl.ucsf.edu> *Date: *Thursday, May 14, 2026 at 2:18 PM *To: *chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> *Subject: *[chimerax-users] Covalently attaching unusual ligands
Hi there, I'm a bioinformatics UCT student and we've been given an assignment to solve a protein structure. Everyone has been struggling with this step and I've tried many many ways to get this to work in ChimeraX, but I get new errors every time so I'm asking for help. Sorry for the long question, but I would *highly* appreciate help at this point (and so would my class - so if I get an answer you'll be making ~30 people very happy, not just 1!)
Essentially this ligand has a sulphur that makes a thioester to Cys 146, our professor said we should remove the Cys sulphur and then combine the ligand and the remainder of the ligand into one residue and name it 'AKG.' We have a dimer so we also do this in 2 places.
We need to refine this using ISOLDE, which is where most of my problems appear. Then he says we can use 'AKG.xml' in residue parameterisation so ISOLDE will accept our residue. Currently the way my pdb is layed out causes chimera to only render the ligand part of AKG but not the Cys part. I don't know why, and more importantly my general understanding of how ChimeraX reads pdb files is lacking.
*So I suppose finally my actual question*: what do I need to do to make it so ChimeraX renders the residue correctly, and ISOLDE accepts AKG.xml and can actually run a simulation on this pdb?
I've attached: 1: AKG.xml (for residue parameterisation) 2: 5 - refine1.mtz (the electron density map data) 3: 6c - part of AKG missing.pdb (the current pdb I'm working with where the Cys part of residue 146 isn't rendered) 4: 6b - pre-covalent linking.pdb (the latest copy of the pdb I could get running in ISOLDE simulations. This has the protein dimer and 2 ligands as 3 separate models. I'd already deleted the Cys's Sulphur here so it's more like an Ala in this case)
Sorry for such a massive email, but I wanted to be as specific as possible with my problem. If you could provide me some help it would be extremely helpful. Sadly our lectures for this module are over and getting our lecturer to explain anything is virtually impossible.
Thanks so much, Byron (and the rest of my class to be honest) _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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