From: Efthymiou, Christos (
Date: Tue Aug 09 2022 - 05:01:28 CDT

I am going to answer my own question in case anyone else experiences a similar problem. After selecting the chain from Chain Type/Selection, I reopened the Structure Manipulation window and chose "Add" and then Apply. This added the chain into the Structure Manipulation window.
From: <> on behalf of Efthymiou, Christos <>
Sent: Monday, August 8, 2022 7:10 PM
To: <>
Subject: vmd-l: Hetero Chain not Recognized by Structure Manipulation Window

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I am using QwikMD to prepare simulation files on a PDB structure which contains a sialic acid. When I load the PDB file into QwikMD, by default the sialic acid chain is not selected and does not appear in the structure manipulation window. However, even after selecting the chain and redoing the structure check, it still does not appear in the structure manipulation window. Without it appearing in the structure manipulation window, I cannot add the necessary topology/parameter files for the sialic acid to continue with preparing the simulation files.

The PDB file I am using was prepared using PDBFixer. However, when I try uploading the original PDB file, 4ONT, from RCSB, the sialic acid chain I would like to use, I, also is not recognized by the structure manipulation window. I have tried searching the contents of the PDB file to see if there is something missing that could explain the chain not registering in the structure manipulation window, but I cannot find anything.

Is there any way to force the structure manipulation window to recognize a chain?

I appreciate any advice.