PDB2PQR 2.1.0 (2015-12) — APBS-PDB2PQR 1.6 documentation

# PDB2PQR 2.1.0 (2015-12)

## New features

- Added alternate method to do visualization using 3dmol.
- Replaced the Monte Carlo method for generating titration curves with Graph Cut. See http://arxiv.org/abs/1507.07021. If you prefer the Monte Carlo Method, please use http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/

## Bug fixes

- Added compile options to allow for arbitrary flags to be added. Helps work around some platforms where scons does not detect the needed settings correctly.
- Fixed broken links on APBS submission page.
- Added some missing files to query status page results.
- Fixed some pages to use the proper CSS file.
- Better error message for `--assign-only` and HIS residues.
- Fixed PROPKA crash for unrecognized residue.
- Debumping routines are now more consistent across platforms. This fixes pdb2pka not giving the same results on different platforms.

## Known bugs

- If more than one extension is run from the command line and one of the extensions modifies the protein data structure it could affect the output of the other extension. The only included extensions that exhibit this problem are resinter and newresinter.
- Running ligands and PDB2PKA at the same time is not currently supported.
- PDB2PKA currently leaks memory slowly. Small jobs will use about twice the normally required RAM (i.e. ~14 titratable residues will use 140MB). Big jobs will use about 5 times the normally required RAM (60 titratable residues will use 480MB). We are working on this.

## Other comments

- Added fabric script used to build and test releases.
- The newtworkx library is now required for pdb2pka.