Hi Alex, Amber certainly used to steal the 6th column of an ATOM record for an extra digit when handling > 99,999 atoms and ChimeraX accepts that treatment. Does Amber do something different now? What does the 100,000th ATOM record look like? --Eric Eric Pettersen UCSF Computer Graphics Lab

On May 6, 2024, at 6:51 AM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi!

I have a large system containing >100k atoms w/o water. Amber produced a pdb file, and I have a trajectory file for it. When I try to open the pdb in chimeraX, most of it loads but with warning "Ignoted bad PDB record on line xxx" and it's all for atom # > 9,999. As a result, when I try to open the .nc file along with the pdb file, the # of atoms don't match anymore.

Alex Lee PhD Student Woods Research Group <https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia

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