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==Alter key bindings== | ==Alter key bindings== | ||
It's not GUI, but you could simply bind a function key such as F1 to a command: | It's not GUI, but you could simply bind a function key such as F1 to a command: | ||
| Line 5: | Line 4: | ||
cmd.set_key('F1',lambda :cmd.show('sticks')) | cmd.set_key('F1',lambda :cmd.show('sticks')) | ||
</source> | </source> | ||
| + | |||
| + | ==Coloring Surface with Electrostatic Potential== | ||
| + | You have to load the potential data by Delphi or some other program like AMBER version 9: | ||
| + | <source lang="python"> | ||
| + | load sample.pdb, molecule | ||
| + | load sample.delphi, potential | ||
| + | show surface, molecule | ||
| + | ramp_new level, potential, [-7,0,7] | ||
| + | set surface_color, level, molecule | ||
| + | </source> | ||
| + | |||
| + | ==Van der Waals radii== | ||
| + | van der Waals Radii are hard coded in Pymol. | ||
| + | They may be obtained for given atoms from: | ||
| + | <source lang="python"> | ||
| + | iterate (name C), print vdw | ||
| + | </source> | ||
| + | Default values are: | ||
| + | *C : 1.70 | ||
| + | *O : 1.52 | ||
| + | *N : 1.55 | ||
| + | *H : 1.20 | ||
| + | *P : 1.80 | ||
| + | |||
| + | and may be changed with the command [[alter]] | ||
| + | |||
| + | ==Tutorial for Beginners== | ||
| + | I'm in the process of writing a PyMol tutorial for first time users. Intended for undergraduate biology/biochemistry students with no previous visualization experience, it will focus on common operations and practical uses. For now, I'm calling it [[Practical Pymol for Beginners]]. I'm not sure where to categorize it. | ||
Latest revision as of 01:29, 28 March 2014
Alter key bindings
It's not GUI, but you could simply bind a function key such as F1 to a command:
cmd.set_key('F1',lambda :cmd.show('sticks'))
Coloring Surface with Electrostatic Potential
You have to load the potential data by Delphi or some other program like AMBER version 9:
load sample.pdb, molecule
load sample.delphi, potential
show surface, molecule
ramp_new level, potential, [-7,0,7]
set surface_color, level, molecule
Van der Waals radii
van der Waals Radii are hard coded in Pymol. They may be obtained for given atoms from:
iterate (name C), print vdw
Default values are:
- C : 1.70
- O : 1.52
- N : 1.55
- H : 1.20
- P : 1.80
and may be changed with the command alter
Tutorial for Beginners
I'm in the process of writing a PyMol tutorial for first time users. Intended for undergraduate biology/biochemistry students with no previous visualization experience, it will focus on common operations and practical uses. For now, I'm calling it Practical Pymol for Beginners. I'm not sure where to categorize it.
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