Some more ligplot love...

While talking to some XRD-working friends I learned that not everyone loves the graphical output that Ligplot produces. However, they do like my previous suggestion about using the ligplot.frm file for further analysis. 

So, trying to provide another useful Ligplot hint I went back digging through the files it produces and I found this other one that seems useful. Let's use one of my favorites the triosephosphate isomerase. This enzyme has been crystallized with many different ligands bound and with the protein in different conformations. For example, 1ney and 1nf0 have the same ligand bound: 1,3-dihydroxyacetonephosphate. Here is the graphical output we all know for 1ney:

 

And the same for 1nf0 (I don't know why I couldn't get the accesibility shading working but I think it is not that relevant):

Now, you could use the *.frm files anf get a nice image such as this one:

 

While this is nice (and you can spot some of the most glaring differences between 1ney and 1nf0) there must be a way to get some names and numbers. Actually, there is. Let's take a look at certain ligplot.sum file for each of the PDBs: 

ligplot.sum for 1NEY

 And:

ligplot.sum for 1NF0

Now, these are very useful giving names, numbers and specifics about the who (mainchain or sidechain) contacts who. And this info is more likely to end up in a useful table in a paper. So, keep an eye on this file.