Hi, My nameis Wes Dennis and I am a retired Geophysicist who is just interested in stuff. I am trying to understand what I am seeing with two ChimeraX images. I applied identical atom-name based coloring commands to the same residue range in two different crystal structures of the same molecule — backbone atoms colored blue, aromatic base atoms colored yellow. The visual result is strikingly different between the two structures. In one, blue color appears to spread into the base panels — a structure in which torsional stresses are present. In the other, where torsional stresses are absent, the base panels are clean yellow with no blue intrusion. My question: does ChimeraX incorporate any geometry-dependent information — bond angles, torsional state, idatm type reassignment based on local environment — into atom rendering or classification that would cause identical coloring commands to produce visually different results across structures? Or is ChimeraX rendering purely atomic positions as recorded in the mmCIF file with no geometry-based modification? Two Images attached Thank you for your help Wes Dennis ------------------------------
