Publication quality figures - Chemdraw and Pymol

I just printed a draft of a couple of my chapters. I have quite a lot of figures in these chapters ranging from graphs made from OriginPro, pictures of my X-ray structure made with Pymol and chemical structures made with Chemdraw. What I immediately noticed was how blurry some of the figures were. It really annoyed me! Like I understand DPIs and all that so why the crappy printing?! So I guess I could've let this slide, I mean I do have better things to do (like write a thesis) but of course I couldn't!

So what I figured out was that my when saving my Chemdraw files as TIFFs the settings on my new computer were off. Instead of >600 dpi it was set at 300 dpi. This is enough of a difference to get blurry pics. Lineart really should be 1000-1200 dpi. So I re-saved all my Chemdraw pics at 1000 dpi. Done.

Onto Pymol.Checking the dpi most pics were around 90 dpi! No wonder they looked blurry! But what did I do wrong? I did ray all my pics. After a quick google search I realised that just hitting the "ray" button isn't good enough (yeh I should've known, but I never really thought about it).

So what I needed were 300 dpi pictures from Pymol. What I did was calculate the resolution of the pic that I required based on the physical size of the picture. (Of course you could have a picture that was much larger than what you really needed and just resize in Word, but the size of each image will also be larger leading to a huge Word file.) For example, if I wanted a 2 x 3 inch image (Yes inches. Annoying for people who work in cm. Just, divide by 2.54 to convert cm to inches) then the resolution I need would be (2*300) x (3*300), which is 600 x 900 dpi. Then I typed (more like copy and pasted) the following commands into Pymol:

ray 600,900;

png picturename.png, dpi=300;

I also changed the antialiasing setting to 2, for higher quality images and also set hash-max to 220 so that it would ray faster (it uses more comp resources. Default is 100).

set antialias, 2
set hash_max, 220

This saves an image called "picturename.png" with a resolution of 300 dpi with a final size of 2 x 3 inches. Viola. Now repeat for the other 30+ Pymol pics...

So the general resolution settings (as I understand from looking at publication guidelines) are as follows:

• Lineart (e.g. Chemdraw, graphs) should be 1000-1200 dpi; 
• Halftone (e.g. Pymol, crystal pics, imaging) should be 300 dpi; and 
• Combination halftones (mix of lineart and halftones) should be 600-900 dpi.

However, if you are preparing figures for a paper, check the journal.

Final words:

• Check the dpi setting on your figures. Make sure that you have the right dpi settings for the right type of pic
• In Word zoom in 500%. If it's blurry it will probably print out blurry.