Protein structure shows a dotted lines hinting about missing residues, but there is no missing residues.

molstar / VSCoding-Sequence

VSCode Extension for interactively visualising protein structure data in the editor

MIT License

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Protein structure shows a dotted lines hinting about missing residues, but there is no missing residues. #14

Open saalim-ihub opened 2 years ago

saalim-ihub commented 2 years ago

hi @a-r-j

I am trying to visualise the protein-ligand complex using Protein Viewer extension, however, it shows dotted lines whereas there are no dotted lines when the structure is viewed in VMD or Chimera. Also, there are no missing residues as per Chimera. What could be the issue and is there any way around it so that it does not show a dotted line? I am using this file for visualisation. 6fnk.zip Screenshot from 2022-10-01 11-40-50

a-r-j commented 2 years ago

Hi @saalim-ihub There are missing residues in the original PDB entry: (See A:GLU:767 - A:GLY:780). This can also be seen on the PDB Mol* viewer

I suspect you've renumbered the residues in your attached PDB file, so whilst your numbering suggests no missing residues, they are in fact still missing!

saalim-ihub commented 2 years ago

Hi, @a-r-j Yes, there are missing residues in the original PDB entry, and I have used Modeller to get the missing residue. I have a few more instances with a similar issue, I will attach some more files soon.