Pyadmin: 4 revisions

2014-03-28T01:06:19Z

4 revisions

New page

Here's an example of using the annotation wizard (see top-left corner):

[[Image:Ann.png|450px]]

<source lang="python">
import pymol

# fetch a protein and setup the view
cmd.fetch("1oky", async=0)
cmd.extract("ligand", "resn STU")
cmd.show_as("sticks", "resn STU")
cmd.show("surface", "ligand")
cmd.flag("ignore", "not rep surface")
cmd.set("surface_color", "grey")
cmd.set("transparency", 0.3)
cmd.distance("(ligand)", "(poly)", quiet=1, mode=2, label=1)

# turn on the annotation wizard + prompt
cmd.wizard("annotation")
cmd.set("wizard_prompt_mode", 1)

pymol.session.annotation = {}

state_dict = {1: ['\\999Molecules:',' \\459staurosporine (ligand)',' \\459protein (1oky)','\\999Objects:',' \\459Hydrogen bond neighbors',]}

pymol.session.annotation["1oky"] = state_dict
</source>

The following source shows you how to use the annotation wizard for multiple objects.

<source lang="python">
import pymol

# fetch a protein and setup the view
cmd.fetch("1oky", async=0)
cmd.extract("ligand", "resn STU")
cmd.show_as("sticks", "resn STU")
cmd.show("surface", "ligand")
cmd.flag("ignore", "not rep surface")
cmd.set("surface_color", "grey")
cmd.set("transparency", 0.3)
cmd.distance("(ligand)", "(poly)", quiet=1, mode=2, label=1)

# turn on the annotation wizard + prompt
cmd.wizard("annotation")

cmd.set("wizard_prompt_mode", 1)
pymol.session.annotation = {}

# using the annotation wizard for multiple objects:

prot_dict = { 1: ['\\999Protein:',' \\459protein (1oky)',]}
lig_dict = { 1: ['\\999Ligand:',' \\459staurosporine (ligand)',]}
dist_dict = { 1: ['\\999Objects: ',' \\459Hydrogen bond neighbors',]}

pymol.session.annotation["1oky"] = prot_dict

pymol.session.annotation["ligand"] = lig_dict

pymol.session.annotation["dist01"] = dist_dict
</source>

[[Category:Wizards]]

Annotation wizard - Revision history

Pyadmin: 4 revisions