[Chimera-users] color of waters using headless version

[Dhananjay]

Dear Elaine,

Thanks for the suggestion.
I reinstalled the headless version (1.13) just to make sure that the
previous installation (version 1.11) is not causing any problem. However,
the waters still changed color to magenta. I could not find any clue where
exactly it went wrong.

Anyway, as per the suggestion, I added two lines, as follows:
color red :WAT & O
color white :WAT & H

and the problem is solved !!!
Thanks again.

Joshi

On Fri, Apr 19, 2019 at 11:06 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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 at 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
>
>

-- 
--------------------------------------------------------------
Dhananjay  Joshi
TIGP Graduate Student
Institute of Biological Chemistry
Academia Sinica, Taipei-115, Taiwan
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