[Chimera-users] on ligand

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 25 10:49:27 PST 2015


Dear Smith,
The rules for which sidechains are shown in the “smart initial display” are the same as for the ribbons preset, 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.”

You cannot change those rules for what is shown automatically except by editing the Python code of Chimera, although you can turn off “smart initial display” entirely (Favorites… Preferences, category: New Molecules).  

However, you probably don’t want to do that.  Instead you could just do what you want with commands.  If you wanted to show all sidechains within 5 angstroms of ligand or ions:

show ligand z<5 | ions z<5

It will be an extra step, however, since it won’t be done automatically when a structure is opened.  To make it easier to apply, you could make this command an alias or a custom preset, which would then show up in the Aliases or Presets menu.  Then you would just have to choose the menu item instead of entering the command.  For example, command

alias ^show5 show ligand z<5 | ions z<5

…will create an Aliases menu with “show5” in it and you would just choose that menu item to apply it.  You could also enter “show5” as a command.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets>

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 Nov 25, 2015, at 3:08 AM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
> 
> When we display a protein-ligand complex by chimera, the sidechains of residues around the ligand will be displayed. Will you please tell me by which criteria chimera select the residues arond the ligand for display? And how to change this criteria in the command input format?
> 
> 
> SMith
> 
> 
>  
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