Generate Image Of Pdb Structure Programmatically

Question

[Kevin]

Hi, I have a list of 1,000 polyproline II helix regions in PDB structures. If I want to view one of them, I load it up in pymol and orient the protein correctly, then highlight the region in a particular color. I would like to do this programmatically without have to open up a viewer.

So far I have tried printing out pymol commands into a text file for each region. I then run the pymol commands all at once and immediately have a view of the molecule but this is still too slow. I need to cut out the view step.

Ideally I will run a script which gives a PDB and a region (res numbers) in the PDB and will be retunred an image of that PDB oriented in the correct way.

Does anyone know of any libraries that will allow me to do this do this? It doesn't really matter what programming language it is in but python would be ideal. Many thanks, Kevin

Answer 1

[Neilfws]

The classic command-line tool for this task is Molscript. It's old, but still works fine.

See my answer to this Generate Image Of Pdb File From Script Or Command Line for more solutions.