Q&A sites are much better than forums or mailing lists for handling technical questions because there is no repetition; each question only gets asked once (how times have you seen the same question on the CCL for example?). If additional information becomes available, that can be added as a new answer (unlike a forum, where adding to an old forum thread is discouraged). Also, if a question is ambiguous, the original author can correct it after some prompting (in a forum, the corrected question may appear half-way down the page).
Anyway, I recently asked the following question which is related to my research:
Given a PDB code, what is the simplest way to get an SDF file with the experimental coordinates of a particular ligand?Matteo Floris provided the answer:
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.)
First, you should download this dictionary (Tabulation of PDB entries containing each chemical component); in this way you can get the full list of ligands associated to PDB entries.
Then, the best is to download the SDF file with all the ligands and use the dictionary for the mapping PDB identifier -> list of associated ligands.
...this gives unique combinations of PDB entry – ligand – PDB entry chain… let me show two examples: the first is the ligand ZU3, for which we have the coordinates in all the PDB where this ligand is present:
the second example, the ligand ZZC, that is present in the SDF file for the same PDB entry but in 2 different chains (A and B):
Now to test it out!