Hi Elaine: That fantastic 'sel sel z<5'! Thanks a lot francesco On Fri, May 12, 2017 at 7:36 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, Although each atom in a residue should have a different name, I guess your model #1.1 has more than one residue. If you hover the mouse over the atom you are interested in, the pop-up information should include both the residue number and the atom name, which you can include in the command to narrow it down, for example:
sel #1.1:2@N z<5
(atom named N in residue 2 of model 1.1). Or, if you don’t mind doing it interactively, you could Ctrl-click to select the atom you want and then use “sel” to specify it, for example:
sel sel z<5
Although you might think that wouldn’t work, it does! 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 May 12, 2017, at 10:26 AM, Francesco Pietra <chiendarret@gmail.com> wrote:
I am trying to investigate the protein surrounding a docked (autodock-vina, alpha chimera 1.1 build 40505 linux 64) ligand. I am interested in the environment of specific atoms of the ligand.
With command
sel #1.1@N z<5
I can investigate the protein at 5A from BOTH nitrogen atoms of model 1.1.
How to select one of the two existing N atoms in the ligand? Same questions for other ligand atoms (there are many O-atoms) Is that possible without elaborating the vina output? thanks francesco pietra