Generate Image Of Pdb File From Script Or Command Line

Question

[NPalopoli]

Hi,

I would like to get an image of a PDB file from any given script or command line order. What tools do you know that could fulfill this task?

Thanks!

Answer 1

[Neilfws]

The classic tool for this purpose is MolScript. Another option is Raster3D, which is easy to install from many Linux repositories (sudo apt-get install raster3d for Ubuntu/Debian-based distros).

There's also a "quick and dirty" trick to fetch images from the PDB website, if you just want a "default" view:

wget http://www.pdb.org/pdb/images/NNNN_asr_r_500.jpg

where NNNN is the PDB code (e.g. 1AOQ).

Answer 2

[Vladimir Chupakhin]

I'd rather use Pymol for that, fist your generate the image you like - save the script (Python) and use it for all other PDBs.

Answer 3

[Jiyao Wang]

You could use iCn3D Python script to get the PNGs: https://github.com/ncbi/icn3d/blob/master/icn3dpython/icn3d_url/batch_export_png.py. You just need to replace the URL in the script.