Hello apbs-users community -
With the release of PyMOL 0.99, a couple of users have asked how to get APBS working with this new version, presumably on Windows. A few people have reported the following error:
ObjectMapLoadDxFile-Error: Unable to open file!
Here are the steps I took to get things working:
1. Download/install PyMOL 0.99.
2. Download/install APBS 0.4.0.
3. Pick your favorite PQR file. For my tests I used PQR files (and not
PDB files which need to be converted within PyMOL prior to using APBS). Alternatively, if you have a PDB file and would like to convert to a PQR
file, I encourage you to use PDB2PQR (see
4. This is the **KEY STEP**. Copy your PQR file and the apbs.exe file to a directory that does NOT contain a space in its name. I believe the default installation location for apbs is C:/Program Files/APBS/apbs.exe - this will not work with the current version of PyMOL. For the rest of these instructions, I'll assume that the C:/pymoltest directory was created and
apbs.exe and a PQR file were placed inside.
5. Open up PyMOL and load in the PQR file that is in C:/pymoltest. For debugging purposes it is useful to use the version of PyMOL with the console window.
6. Open the apbs_tools plugin.
7. Choose "use another PQR", and in the "Choose externally generated PQR" box" point to the PQR file in C:/pymoltest.
8. Click set grid to set the APBS grid.
9. In the APBS Location tab, point the APBS binary to the APBS executable in C:/pymoltest.
10. Click Run APBS - APBS should begin to run. If you have the console window open you will see APBS output, otherwise you'll probably just see a lag until it completes.
11. When complete, go to the visualization tab, click update, and apply whatever visualizations you like.
That should just about do it - remember, the key is that there can be no spaces in the path to the APBS executable or PQR name. Once you get around that step it looks like it should be straightforward. One more note- while these instructions hold for Windows, they might not be necessary on other systems.
Please let me know if you still have any problems -