color of waters using headless version
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
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
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@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@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 --------------------------------------------------------------
participants (2)
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Dhananjay -
Elaine Meng