Closed tuckerburgin closed 6 months ago
I confirm that -m
, --mutation
, and also --mutator
, --mutator-option
, -t
, --thermophile
, -a
, --alignment
, -r
, --reference
, -o
, --pH
, are unused.
Flag was removed in https://github.com/jensengroup/propka/pull/187
There appears to be only very scant documentation on what the
-m
(or--mutation
) flag does or how it is used. As far as I can tell it is only documented in the propka3 command's help text, which says:When I read this it sounds to me like propka will apply the indicated mutation(s) to the specified PDB file and then make a pKa prediction on that mutant structure. In practice, however, this option appears to be doing nothing. For example, here I am calling it with the intention to mutate Asn-64 in my file "stability.pdb" to an aspartate residue:
The above
diff
produces no output; the files are identical. There's no terminal output from propka either, and I can't identify any other files that have been changed. I've also tried this with various syntax changes and settings for the equally mysterious--mutator
and--mutator-option
flags, to no avail. So: what does the-m
option do, and does propka3 in fact have a built-in protein mutator function that does what I think-m
is supposed to do?Here's the relevant snippet of stability.pdb, for reference: