Given a PDB code, what is the simplest way to get an SDF file with the experimental coordinates of a particular ligand?
My current procedure is to go to the PDB Ligand Expo, and use the “Search for instances of chemical components by 3-letter ID code” at the bottom with “PDB entry codes + coordinates files” chosen. This requires me to specify the 3-letter ID code, which I need to have obtained from the web page for the PDB file.
On the search results page, I can simply click on the SDF file for the particular PDB file in which I am interested to download the experimental coordinates.
Is there an easier way? For example, it does not seem to be possible to go directly from the website for a particular PDB entry.
(I would also be interested in the same question applied to a handling a large number of PDB codes at the same time.)
Matteo Floris [ Editor ]
First, you should download this dictionary (Tabulation of PDB entries containing each chemical component);