Ronald Kaback*,†,‡,§ †ĭepartment of Physiology, ‡Department of Microbiology, Immunology, and Molecular Genetics, and §Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095-7327, United States ABSTRACT: The sucrose permease (CscB) and lactose permease (LacY) of Escherichia coli belong to the oligosaccharide/H+ symporter subfamily of the major facilitator superfamily, and both catalyze sugar/H+ symport across the cytoplasmic membrane. Under the Configuration tab of the PyMOL APBS Tools window, customize the remaining parameters the defaults are usually OK.Sugar Recognition by CscB and LacY Junichi Sugihara,† Irina Smirnova,† Vladimir Kasho,† and H. The default values are usually sufficient for all but the most highly charged biomolecules. Under the Configuration tab of the PyMOL APBS Tools window, press Set grid to set the grid spacings. This can be useful if you want to save the generated files for later use. Under the Temporary File Locations tab of the PyMOL APBS Tools window, customize the locations of the various temporary files created during the run. It is not necessary to provide a path to the APBS psize.py binary for most biomolecules. Under the APBS Location tab of the PyMOL APBS Tools window, either browse to (via the APBS binary location: button) or input the path to your local APBS binary.
This step is necessary to ensure you use the radii and charges assigned by PDB2PQR. Under the Main tab of the PyMOL APBS Tools window, select Use another PQR and either browse to (via the Choose Externally Generated PQR button) or input the path to your PQR file. Go to Plugin → APBS Tools… to open the APBS calculation plugin. Load your PQR file you created into PyMOL ( File → Open…) and choose your favorite graphical representation of the molecular structure.
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