Get all residue numbers from the paper figure and put them in your script. The following command will show sticks for residues D443 and Y447 of Importing 13, and color non-carbon atoms with a by-element coloring scheme: show sticks, chain F and resi 443+447 Those are close-ups on inter-chain contacts, for which it shows stick representation of the involved residues. " part in the script with the output from "get_view".įinally, run the script again to generate a 10x10cm ray traced PNG image.Ĭreate 3 sub-figures with the same scriptīased on the previous script (figure 2 B), create the sub-figures A, B and C from figure 4 in the same paper. Set the view interactively in PyMOL using the mouse, then type into the PyMOL command line: get_view
#Pymol tutorial scripts how to#
See for how to use the command.īased on the script for figure 2 A from the previous exercise, create figure 2 B using the following data:
Use the png command to export a 10x10cm PNG image file at 300 DPI. # TODO: ray trace 10x10 cm PNG image at 300 DPI We use an existing script, only the PNG export is missing there.Ĭopy and paste the following script to a file named fig2A.pml. In this exercise we export a ray-traced high-resolution PNG image from PyMOL.
We will reproduce some images from Bono et al. Advanced Scripting Workshop Part 3: Figure scripting by example
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