Please send ChimeraX questions to Chimerax-users@cgl.ucsf.edu instead of chimera-users@cgl.ucsf.edu to avoid confusing people between the two programs. The view command sets clipping planes, and my guess is that when you zoom, the clipping planes don't adjust accordingly (actually I think that may be a bug, will check with the other developers). At least in my test case, the way to avoid this is to put "clip false" in your view command, e.g. view #1.1 orient clip false; turn z 90 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 16, 2022, at 5:24 AM, Enrico Martinez via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera users! I am using ChimeraX for the visualization of protein-ligand interactions comparing two different pdb structures A - ensemble for doclong; B- X-ray pose:
open A.pdb open B.pdb' match #2 to #1.1 # close all docking poses with the exemption of the first pose: close #1.2-end view wait # hide the protein from X-ray pose keeping only ligand for visualisation: hide #2 & protein cartoon hide #2 & protein surface hide #2 & protein #orient view on the model 1.1 and zoom closer view #1.1 orient; turn z 90 zoom 1.5 wait
The problem is that when I use zoom 1.5 after view #1.1 it hides completely the representation for the molecule on the current GUI. Otherwise, it works fine if I center view on the both A and B: view orient; turn z 90 zoom 1.5
How could I zoom the screen properly after orientation of the view on the first molecule?
Many thanks in advance! Enrico