[Chimera-users] Trivial question

[Elaine Meng]

Hi George,
The default "smart initial display" uses rules similar to the ribbons preset (interactive preset 1).  You can control whether or not  "smart initial display" is used in the Preferences, category New Molecules:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules>

The rules are described in more detail for the preset:
<http://www.cgl.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. Nucleic acids may be shown with special sugar and base representations..."

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 Aug 28, 2012, at 8:39 AM, George Tzotzos wrote:

> It seems that a standard feature of Chimera is upon loading a pdb file of a complex, a number of nearby residues also show up.
> 
> My question is whether there's a rule, let's say a cutoff distance, or other.
> 
> Thanks in advance for any advice on this
> 
> Regards
> 
> George
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