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:

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