Hi Wes, Any representation of the atoms directly (stick, ball-and-stick, sphere) uses exactly the coordinates of the atoms as given in the input file. Only "abstracted" representations such as ribbons with smoothed paths might be away from the actual atomic coordinates given in the file. As to different coloring, it must be that the two files have different atom names or something like that -- the coloring will be applied exactly to whatever set of atoms you specified in your command. Coloring does not automatically relate to torsional stress or any other property. Sometimes (depending on molecule size) the default coloring when you initially display the molecule is by heteroatom (nitrogens blue, oxygens red, etc.) but if you actually gave a coloring command like "color yellow" it should do exactly as you say. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 14, 2026, at 6:59 PM, Wes Dennis via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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 <image - Copy.png><image (2) - Copy.png>