#Pymol tutorial chain movie
#Pymol tutorial chain install
#Pymol tutorial chain series
#Pymol tutorial chain download

Very good quality animation but very slow to produce all the PNG files!!Ĥ. If you want ray-traced rendering for all the frames, you can: This will create frame0001.png frame0002.png, etc … This command rotates the protein molecule 360 deg in 60 frames This command rocks the protein molecule +/- 180 degree in 60 frames

#Pymol tutorial chain movie

This command creates a movie with 60 frames PyMOL> color purple, ss h color yellow, ss s color green, ss “”

#Pymol tutorial chain series

Create a series of PNG files for animated GIF movie positively charged) on the protein molecule? That’s is the active site of PH acylphosphatase that binds a negatively charged substrate.Ĥ. Now change the default setting to -10 and +10, and press the “Show” button again.Ĭan you find a craddle with blue surface (i.e. The default setting is: Blue surface: +1 kT Red surface: -1 kT Press the “Show” Button in the Molecular Surface menu. Using PyMOL to visualize the electrostatics map You should be able to see the following results:Ĭoarse grid dims = 53.011 x 58.568 x 65.807 Aįine grid dims = 51.183 x 54.452 x 58.710 A Use psize.py to determine the grid dimensions for APBS calculation The PQR file will be output to pymol.pqr.Ģ. > pdb2pqr.py –ff=amber –apbs-in 1w2i_nowat.pdb pymol.pqr Use PDB2PQR to convert the PDB format to PQR format

#Pymol tutorial chain install

We assume you have install APBS and PDB2PQR in a linux machine.ġ. Using APBS to calculate the electrostatics map You need to remove the water and ligands molecule from 1w2i.pdb.Ī. Using APBS and PyMOL to display the electrostatics surface PyMOL> distance resi 20 and name NH2 and chain A, resi 1092 and name O2 and chain Aģ. You can also measure the distance between two atoms by: When you are finished, press the ‘Done’ button Use this to measure the distance between the arginine N atoms and the oxygen atoms of formate ion. PyMOL> show sticks, (active and sidechain)Ĭlick two atoms to obtain the distance between these two atoms clicked. PyMOL> select sidechain, not (name c+n+o) Display the side-chain of active site residues on top of the cartoon representation PyMOL> select ligand, active around 3.5 and resn FMTĩ. Locate and display the bound formate ion in the active site. If you haven’t rotated the molecule, you can rotate it using the following commands to get a better view of the cradle:ħ. Do you see a hole around the yellow surface? That’s the active site craddle for binding phosphate. PyMOL> select active, (resi 14-20,38 and chain A) 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 chain 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: