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