PDB2PQR 1.6 (2010-04) — APBS-PDB2PQR 1.6 documentation

# PDB2PQR 1.6 (2010-04)

## New features

- Added Swanson force field based on Swanson et al paper (http://dx.doi.org/10.1021/ct600216k).
- Modified printAtoms() method. Now “TER” is printed at the end of every chain.
- Added Google Analytics code to get the statistics on the production server.
- Modified APBS calculation page layout to hide parameters by default and display PDB ID
- Added “make test-webserver”, which tests a long list of PDBs (246 PDBs) on the production PDB2PQR web server.
- Removed `nlev` from `inputgen.py` and `inputgen_pKa.py` as nlev keyword is now deprecated in APBS.
- Added PARSE parameters for RNA, data from: Tang C. L., Alexov E, Pyle A. M., Honig B. Calculation of pKas in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides. Journal of Molecular Biology 366 (5) 1475-1496, 2007.

## Bug fixes

- Fixed a minor bug: when starting `pka.py` from pdb2pka directory using command like “python pka.py [options] inputfile”, we need to make sure scriptpath does not end with “/”.
- Fixed a bug which caused “coercing to Unicode: need string or buffer, instance found” when submitting PDB2PQR jobs with user-defined force fields on Opal based web server.
- Fixed a bug in `main_cgi.py`, now Opal-based PDB2PQR jobs should also be logged in `usage.txt` file.
- Updated `src/utilities.py` with a bug fix provided by Greg Cipriano, which prevents infinite loops in analyzing connected atoms in certain cases.
- Fixed a bug related to neutraln and/or neutralc selections on the web server.
- Fixed a special case with `--ffout` and 1AIK, where the N-terminus is acetylated.
- Fixed a bug in `psize.py` per Michael Lerner’s suggestion. The old version of `psize.py` gives wrong cglen and fglen results in special cases (e.g., all y coordinates are negative values).
- Fixed a bug in `main_cgi.py`, eliminated input/output file name confusions whether a PDB ID or a pdb file is provided on the web server.
- Fixed a bug which causes run time error on the web server when user-defined force field and names files are provided.
- Fixed a bug in `apbs_cgi.py`: pdb file names submitted by users are not always 4 characters long.