Per-Model Lighting Options
I am trying to render different parts of my model in different styles. This is done to emphasize changes in a ligand's force field between different simulations. I would like every part of my model to be rendered in "full", and only change the style for my ligand so it will appear either as "flat", with or without a "silhouettes" toggled on. Is there an option to do this? I would like to just render my custom residue "DIO" in the "flat" style. As you can see from the output it is part of chain 1: " ...Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) ..." I tried to use the following command to separately render different parts of a chain: lighting model #1:DIO flat from the console: >lighting modell #1:DIO flat Expected a keyword while selecting DIO fro the select menu and then running : lighting flat changes the style on the whole image. P.S. full output command when I loaded the molecule: open .\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb" format pdb coordsets true Summary of feedback from opening C:\Users\yis\Desktop\Wenwei Lab\article\first_draft_figs\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb warnings Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV ... 1997 messages similar to the above omitted dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb title: PH06_elaxed_rank_001_alphafold2_translated_100_xyz.pdbqt in water t= 0.00000 step= 0 [more info...] Chain information for dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 Chain Description ? No description available Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) FE2 — (FE2) dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb has 1001 coordinate sets
Hello, Sorry no, the lighting presets (flat, full, soft, etc.) are "global" in ChimeraX, meaning that they apply to everything in the scene. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> The only lighting options that can be changed per model are described in the usage for the "lighting model" command, namely: depthCue, directional, shadows and multiShadow: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html#model> You might try to save two separate images from ChimeraX, and then composite them in some other program like Gimp or Photoshop, but I don't know if that would give the appearance that you want. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 19, 2024, at 3:56 PM, ygilron--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I am trying to render different parts of my model in different styles. This is done to emphasize changes in a ligand's force field between different simulations. I would like every part of my model to be rendered in "full", and only change the style for my ligand so it will appear either as "flat", with or without a "silhouettes" toggled on. Is there an option to do this?
I would like to just render my custom residue "DIO" in the "flat" style. As you can see from the output it is part of chain 1: " ...Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) ..."
I tried to use the following command to separately render different parts of a chain: lighting model #1:DIO flat from the console:
lighting modell #1:DIO flat Expected a keyword while selecting DIO fro the select menu and then running : lighting flat changes the style on the whole image.
P.S. full output command when I loaded the molecule:
open .\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb" format pdb coordsets true Summary of feedback from opening C:\Users\yis\Desktop\Wenwei Lab\article\first_draft_figs\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb warnings Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV ... 1997 messages similar to the above omitted dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb title: PH06_elaxed_rank_001_alphafold2_translated_100_xyz.pdbqt in water t= 0.00000 step= 0 [more info...]
Chain information for dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 Chain Description ? No description available Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) FE2 — (FE2) dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb has 1001 coordinate sets
HI Elaine, Thank you for your timely answer. Any chance you can help me with getting across this graphic point in a different way? Is there a way to see both a surface and cartoon as transparent, with a non transparent ligand showing through? I tried with different colors for cartoon and surface, but I can only see the outline of the surface and the cartoon is invisible even when I do: transparency 30 c transparency 70 s Yet when I do this the cartoon becomes invisible, unless I hide the surface. Best, Yishai On Mon, Aug 19, 2024 at 4:19 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello, Sorry no, the lighting presets (flat, full, soft, etc.) are "global" in ChimeraX, meaning that they apply to everything in the scene. < https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
The only lighting options that can be changed per model are described in the usage for the "lighting model" command, namely: depthCue, directional, shadows and multiShadow: < https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
You might try to save two separate images from ChimeraX, and then composite them in some other program like Gimp or Photoshop, but I don't know if that would give the appearance that you want.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 19, 2024, at 3:56 PM, ygilron--- via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
I am trying to render different parts of my model in different styles. This is done to emphasize changes in a ligand's force field between different simulations. I would like every part of my model to be rendered in "full", and only change the style for my ligand so it will appear either as "flat", with or without a "silhouettes" toggled on. Is there an option to do this?
I would like to just render my custom residue "DIO" in the "flat" style. As you can see from the output it is part of chain 1: " ...Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) ..."
I tried to use the following command to separately render different parts of a chain: lighting model #1:DIO flat from the console:
lighting modell #1:DIO flat Expected a keyword while selecting DIO fro the select menu and then running : lighting flat changes the style on the whole image.
P.S. full output command when I loaded the molecule:
open .\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb" format pdb coordsets true Summary of feedback from opening C:\Users\yis\Desktop\Wenwei Lab\article\first_draft_figs\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb warnings Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV ... 1997 messages similar to the above omitted dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb title: PH06_elaxed_rank_001_alphafold2_translated_100_xyz.pdbqt in water t= 0.00000 step= 0 [more info...]
Chain information for dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 Chain Description ? No description available Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) FE2 — (FE2) dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb has 1001 coordinate sets
Hi Yishai, (I changed the subject line). Sorry, you can't show another transparent thing behind a transparent thing in ChimeraX. This is a limitation, see the section at the bottom of this page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#transparen...> As mentioned in the section linked above, you might instead try showing the surface as mesh, but not transparent. E.g. command transparency 0 surface surface style mesh See surface style help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#style> Or, you could keep the surface as transparent solid surface but make the ribbon thinner so it doesn't block as much, e.g. surface style solid transparency 50 surface cartoon style width 1.0 See cartoon style help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style <mhttps://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style><; I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 20, 2024, at 10:36 AM, Yishai Gilron via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
HI Elaine, Thank you for your timely answer.
Any chance you can help me with getting across this graphic point in a different way? Is there a way to see both a surface and cartoon as transparent, with a non transparent ligand showing through?
I tried with different colors for cartoon and surface, but I can only see the outline of the surface and the cartoon is invisible even when I do: transparency 30 c transparency 70 s Yet when I do this the cartoon becomes invisible, unless I hide the surface. Best, Yishai
Thanks thats very helpful! Best, Yishai On Tue, Aug 20, 2024, 11:06 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yishai, (I changed the subject line). Sorry, you can't show another transparent thing behind a transparent thing in ChimeraX. This is a limitation, see the section at the bottom of this page: < https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
As mentioned in the section linked above, you might instead try showing the surface as mesh, but not transparent. E.g. command
transparency 0 surface surface style mesh
See surface style help < https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...
Or, you could keep the surface as transparent solid surface but make the ribbon thinner so it doesn't block as much, e.g.
surface style solid transparency 50 surface cartoon style width 1.0
See cartoon style help < https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command... <mhttps://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style><;
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 20, 2024, at 10:36 AM, Yishai Gilron via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
HI Elaine, Thank you for your timely answer.
Any chance you can help me with getting across this graphic point in a different way? Is there a way to see both a surface and cartoon as transparent, with a non transparent ligand showing through?
I tried with different colors for cartoon and surface, but I can only see the outline of the surface and the cartoon is invisible even when I do: transparency 30 c transparency 70 s Yet when I do this the cartoon becomes invisible, unless I hide the surface. Best, Yishai
participants (3)
-
Elaine Meng -
ygilron＠asu.edu -
Yishai Gilron