From: jiali wang (jialiwangnamd_at_gmail.com)
Date: Mon Jan 13 2020 - 17:31:33 CST

sometime, if you load psf file first, it will fix that problem
Jiali

On Mon, Jan 13, 2020 at 04:49 Igor Leontyev <ileontyev_at_ucdavis.edu> wrote:

> Hi,
> 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:
>
>
> https://webcache.googleusercontent.com/search?q=cache:V0-8eqcYkToJ:https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/27310.html+&cd=1&hl=en&ct=clnk&gl=us
>
>