I have just started learning Pymol and want to import my images into illustrator in order to make figures, but when I bring the figures in they are of lower quality than the PNGs show.
I am taking images with highest quality and ray imaging on pymol and they look great when I bring them into powerpoint, but they look terrible in Illustrator.
Also I have to drag and drop the files in order to get a transparent background, if I copy from the PNG viewer I get an opaque background, same when I just copy the image to clipboard after taking. This is consistent in illustrator and powerpoint and I have made sure that the transparent background option is on in Pymol.
I have also checked I'm not using pixel preview on Illustrator.
I was able to get a good image by opening the PNG in Illustrator but I can't then copy it to another sheet without the same pixelation issues and I need multiple structures on one sheet.
I can't find anything online that matches my issue.
If anyone has any advice on either issue it would be great.
I recommend saving your PyMOL images as ray-traced svg files. Then, you can import these into a vector-based program such as Adobe Illustrator or Inkscape for further processing.
To get high-quality PyMOL images into Adobe Illustrator, first optimize your PyMOL scene for clarity—set the background to white with "set bg_rgb=[1,1,1]", boost antialiasing via "set antialias, 4", disable fog and shadows if needed ("set ray_trace_fog=0; set ray_shadows=0"), and enable a black outline for better contrast using "set ray_trace_mode, 1". Then, render a high-resolution image with the "ray" command (e.g., "ray 2400,2400" for an 8-inch image at 300 DPI) and export as PNG using "png filename.png, dpi=300". Since PyMOL doesn't export true vectors directly, import the PNG into Illustrator as a placed file for raster use, or for editable vectors, apply Image Trace (Object > Image Trace > Make, then tweak settings like Preset: High Fidelity Photo) to convert it—though this can be time-consuming for complex structures. Alternatively, trace the PNG in free software like Inkscape to SVG first (using Path > Trace Bitmap with multicolor mode and 8-10 scans), then open the SVG in Illustrator for finer edits. If starting over, consider tools like VMD or VESTA for direct SVG export from your PDB file.
Sam Gastrell -- Amir Sedaghati was correct, and my answer was not correct. What I have been doing is ray-tracing from the "Draw/Ray" pull-down menu, selecting "Ray", and then "copy image to clipboard". I then paste the image into Inkscape (or Illustrator) and save it an an svg file. I do final editing, such as adding labels, in PowerPoint, from which I can also export the result in svg format.
- Badges
- Science topic