Dear users, I opened my reference pdb (ref_conf.pdb) and oriented (using ref_conf.mat) as I needed. Next, I opened another pdb (conf_1.pdb) and aligned to the reference with respect to residues 1-110. Then I deleted the reference pdb and hide all the atoms. Nest, I display waters and the atoms of residue 73 and 145 (as I wanted to show). The image is then saved. All the commands that I used are put in test.com file, as follows: open ref_conf.pdb matrixset ref_conf.mat open pdb/conf_1.pdb mm #0:1-110 #1:1-110 delet #0 ~display #1 @ display :WAT display :73@ display :145@ color magenta,r helix; color yellow,r strand; color gray,r, coil copy file temp2png.png png width 1200 height 1000 stop I run the following command: chimera test1.com When I used with GUI version 1.11 (build 41141) of Chimera, everything goes well and the saved png is exactly as I wanted. However, when I used the headless version (version 1.13.1 (build 41965) ) the waters' color changed to magenta. I don't know why the color of waters changed and does not remained as default colors (i.e. red for oxygen and white for hydrogens). Am I missing something in the above script or this is a bug with headless version? Thanks. Joshi