From: Igor Leontyev (
Date: Mon Jan 13 2020 - 03:18:45 CST

I came across of the following issue. I cannot view in VMD the full
protein chain in cartoon, trace or tube representation (few helices out
of 10 are not shown). While with lines and bonds the entire chain is shown.

Probably the code does not recognize the protein fragments beyond some
point. This looks like a bug. I will try to explain why.

I have two PDB files of the same protein which differs from each other
only by rotation and shift. One of them is shown correctly and another
is NOT. In fact the second was obtained from the first one by aligning
it to some other protein and saving PDB in VMD.

Another test. Same alignment and saving was repeated in PyMol. The
resulting PDB structure in VMD again was not shown correctly. But in
PyMol both structures after reloading PDBs looks good. This is an
indication that the issue probably is on VMD side.

If interested I can upload those two structures for debugging.

Same issue was reported previously on VMD-l, see link: