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Electrostatics
Cube to/from DX File conversion
I'd like to be able to convert between Gaussian Cube File format and DX File format
Still new to APBS ...
In my .in file I tried: 'write pot cub' and 'write pot cube' neither worked -- could you tell me the correct form?
thanks,
Scott
Scott Bembenek, Founder, CEO, CSO Denovicon Therapeutics https://www.denovicontx.com/ 1130 Wall St #558 La Jolla, CA 92037 https://www.denovicontx.com/
On Tue, Mar 16, 2021 at 7:06 PM Nathan Baker @.***> wrote:
APBS can read/write both; what are you looking for?
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That's odd -- for some reason I thought it was supported natively in APBS but it isn't listed in our documentation (https://apbs.readthedocs.io/en/latest/using/input/elec/write.html).
@intendo and @Eo300 -- what do we use in the APBS web interface to generate Cube files for 3dmol?
The only mention of cube is in the FETK software. The documentation seems to indicates that OpenDX is the format for APBS files. @Eo300 sent me the following:
APBS itself only produced the DX files. The cube files came from a script which was run post-APBS called dx2cube.py, with the original found here in the old repo. Brought it over to APBS-REST when I realized it was needed for the visualizer.
The script currently in use: https://github.com/Electrostatics/apbs-rest/blob/master/src/runner/uploader/dx2cube.py
Original (from old repo): https://github.com/Electrostatics/apbs-pdb2pqr/blob/b3bfeecbf4cfd04bf53f983e1a8064ef250bf25f/pdb2pqr/dx2cube.py
Wow; that is a seriously ugly script. I'll create a new issue to upgrade.
Thanks very much for following up on this!
Scott Bembenek, Founder, CEO, CSO Denovicon Therapeutics https://www.denovicontx.com/ 1130 Wall St #558 La Jolla, CA 92037 https://www.denovicontx.com/
On Mon, Mar 22, 2021 at 11:45 AM Nathan Baker @.***> wrote:
Wow; that is a seriously ugly script. I'll create a new issue to upgrade.
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