How to make high-quality protein structure alignment figures
First, use the alignpair command to rotate the query
structure so that it is aligned with the target structures, e.g.:
reseek -alignpair 1hhs.pdb -input2 7c2k.pdb -aln 1hhs_7c2k.txt \
-output 1hhs_rotated.pdb
Load 72ck_rotated.pdb into Pymol
using File, Open.
Load 1hhs.pdb by using File, Open a second time in the same window.
You should see something like this:
For best image quality, select Display, Quality > Maximum Quality.
Set the background color using Display, Background, probably White
or Alpha Checker is best. The Alpha Checker option
gives you a transparent background which is helpful if you're going to be adding
annotations in image editing software such as Gimp
or Inkscape.
Choose colors for the structures by clicking the [C] buttons.
Some transparency may make the superposition clearer (...literally).
For example, if you have chosen a cartoon representation, then you
can go to Setting, Transparency > Cartoon, something like 40%
transparency looks pretty good.
Now you should should have something
like this, which you can save using choose File, Export Image As.
