生物医学A_tutorial_on_using_PyMOL_to_generate_publication_quality_figures[[公众微信号：bioworlde]].PDFVIP

PyMol Tutorial [return to KB Wongs home page] A tutorial on using PyMOL to generate publication quality figures. Through this tutorial, you will be able to generate the following figures: You can download the files for the tutorials here. Files included: 1w2i.pdb - crystal structure of PH acylphosphatase (PDB: 1W2I) (Cheung et al, Biochemistry, 44:4601-4611.) 2fofc.map.xplor - electron density map from CNS/XPLOR (The map file name should include the .xplor extension) .hk/~b102142/pymol/pymol_tutorial.html[2014/6/12 11:19:32] PyMol Tutorial 1w2i_nowat.pdb -The water and ligand molecules from 1w2i.pdb have been removed (for electrostatics calculation). Since PH Acylphosphatase exists as a monomer in solution, only chain A is included. apbs.in - the template APBS input file for electrostatics calculation pymol.dx - the calculated electrostatics map PyMOL can be download from / Remember, if you make figures for publication, please remember to cite: DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA. 1. Figure showing Electron Density Map You will be able to generate the following figure after this tutorial: 1. Loading PDB file File - Open - 1w2i.pdb 2. Load the map file File - Open - 2fofc.map.xplor It takes a while to load the map file. 3. Zoom in the active site PyMOL select active, (resi 14-20,38) and chain A PyMOL zoom active PyMOL hide all PyMOL show stick, active 4. Locate and Display the active site water We know that the amide group of Asn38 is h-bond to an active water. PyMOL select active_water, ( (resi 38 and name ND2 and chain A) around 3.5) and (resn HOH) The above command select any water molecules that is/are around 3.5A of the ND2 atom of resi 38 in chain A PyMOL show spheres, active_water Well the Oxygen atom is now shown in its vdw radius. We can reduce the size of the sphere to 0.