[Chimera-users] color of waters using headless version

[Dhananjay]

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
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