In this tutorial we show, step by step, how to run the MolAxis stand-alone version on three examples.

This pdb file includes several examples of MolAxis server runs with channels emanating from inner chambers and transmembrane (TM) channels.

Beta Barrel Proteins
1. Download from the PDB website the file with code 1PRN.
2. Run molaxis init -pdb 1prn.pdb -e 0.1 -type channel -channel_via 2.817 39.232 34.308 1 -channel_z 0 0 1 -outer_sphere 30. Two files created: 1prn.pma and 1prn.stats_init files.
3. Run VMD (preferably version 1.8.4 or higher) from the directory containing the pdb file and load the PDB file.
4. Open tcl console by Extensions->TK Console and run: source MOLAXIS_PATH/root/script/molaxis.tcl.
5. In the TK Console run MolAxis::view command main.
6. Run molaxis graph -pdb 1prn.pdb -graph_type z -graph_main. Two files are created: 1prn.graph_main and 1prn.graph_main_bottle.
7. You can create the channel graph with programs like MathLab or gnuplot using the file: 1prn.graph_main
* You should get similar figures similar to the following:
ABC Transporter Proteins
1. Download from the PDB website the file with code 2NQ2.
2. Run molaxis init -pdb 2nq2.pdb -e 0.1 -type channel -channel_via 18 -14.5 40.5 4 -channel_z 36 -40 20 -outer_sphere 35. Two files created: 2nq2.pma and 2nq2.stats_init files.
3. Run VMD (preferably version 1.8.4 or higher) from the directory containing the pdb file and load the PDB file.
4. Open tcl console by Extensions->TK Console and run: source MOLAXIS_PATH/root/script/molaxis.tcl.
5. In the TK Console run MolAxis::view command main disp_radius 7.
6. Run molaxis graph -pdb 2nq2.pdb -graph_type z -graph_main. Two files are created: 2nq2.graph_main and 2nq2.graph_main_bottle
7. You can create the channel graph with programs like MathLab or gnuplot using the file: 2nq2.graph_main
* You should get similar figures similar to the following:
Human Cytochrome P450 Enzymes
1. Download from the PDB web site the file with code 1W0E.
2. Run molaxis init -pdb 1w0e.pdb -e 0.3 -rm void -hetatoms HEM -outer_sphere 30. Two files created: 1w0e.pma and 1w0e.stats_init files.
3. Run VMD (preferably version 1.8.4 or higher) from the directory containing the pdb file and load the PDB file.
4. Open tcl console by Extensions -> TK Console and run: source MOLAXIS_PATH/root/script/molaxis.tcl.
5. In the TK Console run MolAxis::view disp_radius 5.
6. Color each pathway in a separate color: a- In the TK Console run MolAxis::view pw X disp_radius 5 for pathway X. b- In the command line run: cp 1w0e_tcl.vmd X.vmd. c- open with a text editor the X.vmd file and change the line graphics 0 color blue/green/red to a desired color and thus coloring a channel with a singe unified color. d- In the TK Console run source X.vmd. e- Reapeat steps in 6. for channels: 0, 1, 3, 5, 6, 7, 8, 9 and color them blue, red, green, orange, yellow, pink, silver, and iceblue respectively. The heme is colored brown and represented as VDW. * You will get a picture similar to the one below.
7. For obtaing graphs of each channel: run molaxis graph -pdb 1w0e.pdb Three files are created: 1w0e.graph_pathway_X 1w0e.graph_pathway_X_bottle 1w0e.graph_pathway_X_all for each pathway.