Hi Alex, Yes, the commands are different in both form and functionality between the two programs. Currently the most similar thing in ChimeraX is to use "view" with "zalign" ... but the intent is to give 2 atoms to align along z, not the whole ligand. For example: open 2gbp view zalign @c1 @c4 ... or maybe ... view ligand zalign @c1 @c4 ...however, that requires knowing the atom names in the ligand and judiciously choosing the right ones. I thought it might be useful if we could generalize that option to allow two multi-atom specifications (such as ligand and ~ligand) and then use the center of each for the axis alignment. We'll see what the other developers say (I'm not a programmer so I wouldn't be the one doing it.) Even so, however, I don't think it would guarantee that there aren't other atoms in front of the ligand, for example if the pocket is completely buried. I also don't think that the Chimera approach you mentioned guarantees that either, although maybe in practice you haven't seen it happen. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 5, 2023, at 7:04 AM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello everyone,
In old Chimera, I was able to center the ligand to the foreground of view using "align ligand ~ligand" no matter the orientation, if the ligand is in view or not. Is there a comparable way in ChimeraX? The same command gives "expected a keyword" and using "view ligand" or "view sel-residues zalign sel" does not bring it to foreground if it's behind something else.
Thanks, Alex