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pHmap tutorial

After installation try to run the examples.

Extract the example.zip and you find three .pdb, a set_view.txt, a activityData.txt and a ligand.mol2 file

Quick start

• For visualizing only surface charges you can type: pHmap *.pdb -r '5 6 0.5' -s set_view.txt -l ligand.mol2
• This will use all pdb files within the folder and calculates charges for a pH range from 5 to 6 with 0.5 steps (pH values: 5.0 5.5 6.0).
• Type: pHmap -h which shows also some other examples…
• This is in principle all you have to do, however before you start with your own proteins you need some prerequisites…

Setup view

• To position your protein in a way you would like to represent it (e.g. so that the cofactor looks into your direction) you have to open your pdb files in PyMol and superimpose all structures, to have the same coordinates.
• Finally, you type get_view and copy the set_view screen output from pymol into a text file.

Prepare ligand

• If your protein contains a cofactor or ligand, which is located close to the surface, it will change the surface electrostatics. Therefore, you have to provide a .mol2 file with the coordinates and atom types.
• Click in pymol on the ligand or cofactor and export it as .mol2 file. It is very important that you export the .mol2 file from the .pdb file you also load to pHmap, otherwise the ligand has other coordinates.

Limitation

• Hence, the ligand within the .pdb file will be ignored, you can only run one ligand file, because pdb2pqr and abps only support one ligand file. If you have different proteins with different ligands, you have to run pHmap for each individual structure.

Re-run pHmap

Update view settings

• If you have succesfully run pHmap, however, the view settings are not optimal, you don’t have to run all calculation again. pHmap can skip different parts of the script, such as the calculation of the electrostatic matrix.
• For that you run the same command again, however with an additional flag argument: pHmap *.pdb -r '5 6 0.5' -s set_view.txt -l ligand.mol2 --update_rendering
• This will skip pdb2pqr and abps calcualtions and only runs pymol rendering and imagemagick again.

Update axis and style

• If you only want to update the axis, because you changed the font size for instance, this is possible by only running imagemagick again: pHmap *.pdb -r '5 6 0.5' -s set_view.txt -l ligand.mol2 --update_axis
• This will skip pdb2pqr, abps and pymol rendering, only collects all pictures and generates the final picture, so you can easily change the axis settings or font settings for example.