Espript : Trouble shooting

I like Espript very much, but it can be confusing when error messages follow your job submissions, and you don't know what you have done wrong. I document my recent experience below so that I may return to this and others may also find it useful.

1. Make sure the sequences in the alignment and PDB are consistent.

Espript looks at both aligned sequences and the PDB files, therefore it will be confused if there is an inconsistency between the sequence in the alignment and the PDB.
Often, the sequences downloaded from RCSB/NCBI are not identical to that in the PDB structure files. This is because not all coordinates can be assigned where electron densities are weak.

In this case, you can use this to extract the amino acid sequence from PDB files. And then you can use it to create a sequence alignment.

Usually this will give you an alignment that will work well for Espript.

If you are still having a problem, read on.

2. Check the quality of the PDB.

Open the "Server logs" tab in the "Results" window. Many clues can be found here if something goes wrong. In my case, the log told me it found this strange "X" amino acid in the PDB I uploaded.

On closer inspection, it turns out that the coordinates of sidechains were missing from some amino acids.
(This is a fairly common crystallographic problem. Sometimes electron densities are too weak for assigning coordinates. Actually, I like the authors' honesty for not assigning coordinates if there are no electron density)

Espript uses DSSP for extracting secondary structure information from PDBs. You can obtain the DSSP file of your PDB, and mine looked like below.

**Tip: I prefer to rename my DSSP file to something like "file.dssp" for clarity.

I "corrected" the DSSP output file by replacing those "X" amino acids by what really are suppopsed to be in those places. So in the case above, the first two "X" were replaced by K and R. Additionally, I had to make sure that the residue numbers are completely contiguous (continuous) in the "RESIDUE" column.

So now you have an edited DSSP file that describes the secondary structure of your PDB file. You can upload this DSSP file to Espript instead of the PDB file, and Espript will work.

These are what I had to go through, and hopefully it may solve your trouble too. Comments are appreciated. Good luck!