Dear Joshi,
I have absolutely no idea why the waters would be a different color using the headless version vs. the GUI version.  I.e. even if you used the same version  number in both cases I would expect the same colors at the end of executing the same script.

However, without understanding the problem, you could try just adding another command to make sure the waters are colored the way you want, e.g.

color byatom :wat

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 18, 2019, at 11:52 PM, Dhananjay <dhananjay.c.joshi@gmail.com> wrote:
>
> 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