[Chimera-users] Displaying side chains

[Elaine Meng]

Hi Manish,
Mark is absolutely right.  This “smart initial display” is in the Preferences , category: New Molecules:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules>

if true, "show subsequently opened molecule models with settings similar to the ribbons preset” … which is in turn described here:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>

"shows most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.”

There is a link from “ligand” in that page to an explanation of how something is classified as a ligand.

Of course, you can still show/hide whatever atoms you want, it is only an initial display meant to help you understand the structure when you first open it.  You can use the all atoms preset (menu: Presets… Interactive 2 (all atoms)) to quickly see all atoms, or you can use commands (display, show, ribbon…) or the Actions menu to show and hide specific parts.  To learn about those possibilities, see the tutorials, such as “Getting Started”:
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



> On Apr 13, 2017, at 12:16 AM, Mark J. van Raaij <mjvanraaij at cnb.csic.es> wrote:
> 
> 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 Raaij
> CNB-CSIC
> wwwuser.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.
> 
> Sincerely
> Manish
>