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Electrostatics / apbs

Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
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Cube to/from DX File conversion #131

Open sbembenek18 opened 3 years ago

sbembenek18 commented 3 years ago

I'd like to be able to convert between Gaussian Cube File format and DX File format

sobolevnrm commented 3 years ago

APBS can read/write both; what are you looking for?

sbembenek18 commented 3 years ago

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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sobolevnrm commented 3 years ago

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?

intendo commented 3 years ago

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.

Eo300 commented 3 years ago

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

sobolevnrm commented 3 years ago

Wow; that is a seriously ugly script. I'll create a new issue to upgrade.

sbembenek18 commented 3 years ago

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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