Yet another tool I'd like to contribute: density-fitness.
Copied from the ITP:
The program density-fitness calculates electron density metrics,
for main- (includes Cβ atom) and side-chain atoms of individual residues.
For this calculation, the program uses the structure model in either PDB
or mmCIF format and the electron density from the 2mFo-DFc and mFo-DFc maps.
If these maps are not readily available, the MTZ file and model can be used
to calculate maps clipper. Density-fitness support both X-ray and electron
This program is essentially a reimplementation of_edstats_, a program
available from the CCP4 suite. However, the output now contains only the
RSR, SRSR and RSCC fields as in_edstats_ with the addition of EDIAm
and OPIA and no longer requires pre-calculated map coefficients.
I cannot run an autopkgtest yet. But now I do know a bit more why:
When I was building libpdb-redo, libnewuoa was already accepted but not
on the build servers yet. Using --extra-package for both gbp
buildpackage as well as sbuild resulted in using my local copy of the
package. For building as well as testing.
But now libpdb-redo is not uploaded yet and not known. When I use the
--extra-package flag for density-fitness it is only used by sbuild
during building the package but ignored when running autopkgtest. gbp
buildpackage completely refuses to build at all claiming it doesn't know
libpdb-redo even though I passed it explicitly.
Apparently, a package must in the catalogue for --extra-package to have
So, whether the autopkgtest of density-fitness works is something is
something I can only find out by booting into a sid myself. But I didn't
do that, yet.