Hi, CCP4bb'ers,
I am having some trouble with Procheck. I am using two different
installations, one that came with CCP4-6.0.2 and the other is procheck
3.5.4 (I think they are the same versions).
Anyway, I can reproducibly get the .out file to correctly report many
bad contacts; however, the .sum file, which is what most of us quickly
checks, always reports zero bad contacts with certain (CNS-type) pdb
files. After a gazillion test runs with procheck, I figured out that
all I need is to have the first residue number to be '0' to get a
false report of zero bad contacts in the .sum file.
All I do is, add this line as the first line in the pdb (presence or
absence of REMARKS makes no difference):
ATOM 1 C GLY A 0 27.769 17.185 79.547 1.00186.88 A
and I get a report of zero bad contacts no matter what the rest of the
file is. If I make the first residue number '1', .sum report is
accurate. And it doesn't matter having/not having overlapping atom
numbers in the pdb, either. Coordinates also do not matter. I went
back to files from another project, and changing the first residue
number to '0' in an unrelated file resulted in the same outcome/bug.
Just adding that line above, does not make it for the unrelated pdb,
however.
The question is: Is this possible, and can anyone reproduce it, or
have I gone completely mad?
Happy holidays,
Engin
P.S. Another issue I observed before with procheck was, I think, that
MSE (selenomethionine) was giving bad contacts with the neighboring
residues (not with the neighboring main chain atoms, but the ones
after them - not exactly sure, though).
