[Chimera-users] Displaying side chains

Mark J. van Raaij mjvanraaij at cnb.csic.es
Thu Apr 13 00:16:15 PDT 2017

As I understand it, Chimera by default displays those side-chains that are near ligands, and assumes that any non-water, non-protein molecule is a ligand.
Mark J van RaaijCNB-CSICwwwuser.csic.es/~mjvanraaij
-------- Original message --------From: Manish Manish <manishjnu8 at gmail.com> Date: 13/04/2017  08:55  (GMT+01:00) To: Chimera-users at cgl.ucsf.edu Subject: [Chimera-users] Displaying side chains 
I have opened  PDB ID 1iep using "fetch structure by ID from PDB" through chimera GUI menu. I can see the side chain of few residues such as PHE 317.A and Valine 299.A are automatically displayed. Also by moving the mouse cursor, one can find the distance between different atom types such as between CA and CB. Whereas side chain of many residues such as Lysine 274.A and ASP.276 have not been displayed.

My question is how the chimera decides this differential display? Whether chimera directly uses information from PDB files to differentially display the side chains and distance. Or chimera has its own algorithms to decide this. It will be a great help for me if one can point me toward the portions of PDB file or source code from Chimera which does this.

I have also attached the image file.


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