You can set the surface to be partially transparent. Hide everything and then show protein cartton You will be able to generate the following figures after this tutorial:Ģ. If you have done everything right, you should be able to see this: You will be able to preview the low resolution figures on screen.
To render a figure with the default resolution (640×480) Normally you want to set the background color to white for publication You can change the color of the map by:ħ. PyMOL> isomesh mesh1, 2fofc.map, 1.0, active, carve=1.6Ħ. PyMOL> isomesh mesh1, 2fofc.map, 1.0, (resi 14-20,38 and chain A), carve=1.6īecause the residue atoms were previously defined as “active”, you can simply type: Display the electron density around the active site atoms at sigma level=1.0 We can reduce the size of the sphere to 0.5A by:ĥ. Well the Oxygen atom is now shown in its vdw radius. The above command select any water molecules that is/are around 3.5A of the ND2 atom of resi 38 in chain A PyMOL> select active_water, ( (resi 38 and name ND2 and chain A) around 3.5) and (resn HOH) We know that the amide group of Asn38 is h-bond to an active water. PyMOL> select active, (resi 14-20,38) and chain AĤ. You will be able to generate the following figure after this tutorial: The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA.
Remember, if you make figures for publication, please remember to cite:ĭeLano, W.L. Pymol.dx – the calculated electrostatics map Since PH Acylphosphatase exists as a monomer in solution, only chain A is included.Īpbs.in – the template APBS input file for electrostatics calculation xplor extension)ġw2i_nowat.pdb -The water and ligand molecules from 1w2i.pdb have been removed (for electrostatics calculation).
Pymol tutorial align download#
You can download the files for the tutorials here.ġw2i.pdb – crystal structure of PH acylphosphatase (PDB: 1W2I) ( Cheung et al, Biochemistry, 44:4601-4611.)Ģ – electron density map from CNS/XPLOR (The map file name should include the. Through this tutorial, you will be able to generate the following figures:
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