Hi Maarten, The “smart initial display” just shows sidechains near ligands, as a guess of what might be interesting to see initially. It uses the same criteria as the ribbons preset: “... residues within 3.6 Å of a ligand residue or metal ion” smart initial display is set on/off in the New Molecules preferences: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules> presets: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets> You could certainly display a zone using a different distance cutoff, and/or run contact and H-bond calculations if you want to seriously analyze the interactions. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html> I hope this clarifies, 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 Oct 26, 2016, at 5:56 AM, Maarten Schledorn <m.schledorn@gmail.com> wrote:
Dear reader,
I have a pdb file of a protein with bound ADP and the file contains nothing but atomic coordinates and a few CONECT lines. If I open the file, the residues involved in binding ADP are shown, but I would like to know how Chimera knows this. I assume it is some VdW vicinity/overlap perhaps, or all residues within a certain distance from the ADP molecule, but I would like to know exactly how it is defined. I have tried to look for it in the documentation but haven't been successful so far. Does someone know the answer or a link to where it has been discussed previously?
Many thanks in advance! Maarten