On Aug 3, 2009, at 5:01 PM, Elaine Meng wrote:
If you did want the exact charges from PDB2PQR, you could reformat
those charges (next-to-last column in the original PQR file) into an
attribute assignment file and reassign them with Define Attribute (or
command defattr), after reading in the edited PDB files (PQR files
with last 2 columns removed).
In this vein, I wrote a Python script (pqr2chimera.py) that will read a PQR file and output a PDB file that Chimera can read (chimera.pdb) and a defattr file (chimera.defattr) that could be used to assign the PQR charges to the model, if for some reason you prefer them to the charges that Chimera would assign. The script is attached. You run it from a Unix shell like this:
python pqr2chimera.py my_pqr_file.pqr
The two output files will appear in the directory you run it in. One caveat is that since the defattr output file uses "@/serialNumber=" as it's atom selector, defining the charge attribute in Chimera using that file is kind of slow -- it looks through the list of atoms every time to locate the one with the matching serial number. It probably would be faster if the selector were written in the ":res@atom" form, but since I'm not even sure you care about the defattr part I took the lazy road.
--Eric