MacOSX-specific .pymolrc file - Revision history

Pyadmin: 4 revisions

2014-03-28T01:53:13Z

4 revisions

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Here is an example of a ~/.pymolrc file that [[User:Wgscott|I]] use on Mac OS X. There are two main things going on here:

* It defines a bunch of aliases, including one that ribbonizes protein/nucleic acid comples (this could benefit from updating)

* It runs a series of pythonized pymol commands to permit interaction with the [[MAC_Install#PowerMate_Dial | PowerMate Dial]]

<source lang="python">

_ feedback push
_ feedback disable,all,everything

alias clear, mstop; mclear; hide all
alias nogui, set internal_gui=0
alias gui, set internal_gui=1
alias shiny, set spec_power=250; set spec_refl=1.5; set antialias=1; ray
alias grab, os.system("open -a Grab")
alias stop, quit
alias exit, quit
alias white, bg_color white; set depth_cue=0; set ray_trace_fog=0

from pymol import cmd

# Define aliases for mapping in [x,y,z] rotations and translations into a single Powermate
# dial. Toggling between the three is possible if you then assign these to special keys.

# Functions for x,y,z rotations and translations using Powermate dial
# Program F1 and F2 for Rotate Right and Rotate Left
# Program F3 and F4 for Click & Rotate Right and Click & Rotate Left
# Program F5 for Click (to toggle between dialsets)

# dialset = 2

def dialx(): \
global dialset \
dialset = 1 \
cmd.set_key ('F1', cmd.turn,('x',-2.0)) \
cmd.set_key ('F2', cmd.turn,('x',2.0)) \
cmd.set_key ('F3', cmd.move,('x',-0.5)) \
cmd.set_key ('F4', cmd.move,('x',0.5)) \
print "dialset ", dialset, " [ X ]\n" \
return dialset

def dialy(): \
global dialset \
dialset = 2 \
cmd.set_key ('F1', cmd.turn,('y',-2.0)) \
cmd.set_key ('F2', cmd.turn,('y',2.0)) \
cmd.set_key ('F3', cmd.move,('y',-0.5)) \
cmd.set_key ('F4', cmd.move,('y',0.5)) \
print "dialset ", dialset, " [ Y ]\n" \
return dialset

def dialz(): \
global dialset \
dialset = 3 \
cmd.set_key ('F1', cmd.turn,('z',-2.0)) \
cmd.set_key ('F2', cmd.turn,('z',2.0)) \
cmd.set_key ('F3', cmd.move,('z',-0.5)) \
cmd.set_key ('F4', cmd.move,('z',0.5)) \
print "dialset ", dialset, " [ Z ]\n" \
return dialset

def toggle_dial(): \
if dialset == 1 : \
print "Changing to y" \
dialy() \
elif dialset == 2 : \
print "Changing to z" \
dialz() \
elif dialset == 3 : \
print "Changing to x" \
dialx() \
else: print "Dial assignment isn't working"

cmd.set_key ('F5', toggle_dial)

# Start default dial state for rotate y (arbitrary choice)

dialy()

alias ribbonize,\
hide; show cartoon; set cartoon_fancy_helices, 1; \
hide cartoon, ( resname A or resname G or resname C or resname U or resname T ); \
show sticks, ( resname A or resname G or resname C or resname U or resname T ); \
util.rainbow; color hotpink, ( resname A or resname G or resname C or resname U or resname T )

# END COMMANDS
_ feedback pop

print "PowerMate Dial interface has been enabled"

print "Finished reading ~/.pymolrc"

</source>

[[Category:Mac]]
[[Category:Launching]]

Wgscott at 19:08, 18 February 2006

2006-02-18T19:08:48Z

Wgscott at 19:01, 18 February 2006

2006-02-18T19:01:31Z

New page

<source lang="python">

_ feedback push
_ feedback disable,all,everything

alias clear, mstop; mclear; hide all
alias nogui, set internal_gui=0
alias gui, set internal_gui=1
alias shiny, set spec_power=250; set spec_refl=1.5; set antialias=1; ray
alias grab, os.system("open -a Grab")
alias stop, quit
alias exit, quit
alias white, bg_color white; set depth_cue=0; set ray_trace_fog=0

from pymol import cmd

# Define aliases for mapping in [x,y,z] rotations and translations into a single Powermate
# dial. Toggling between the three is possible if you then assign these to special keys.

# Functions for x,y,z rotations and translations using Powermate dial
# Program F1 and F2 for Rotate Right and Rotate Left
# Program F3 and F4 for Click & Rotate Right and Click & Rotate Left
# Program F5 for Click (to toggle between dialsets)

# dialset = 2

def dialx(): \
global dialset \
dialset = 1 \
cmd.set_key ('F1', cmd.turn,('x',-2.0)) \
cmd.set_key ('F2', cmd.turn,('x',2.0)) \
cmd.set_key ('F3', cmd.move,('x',-0.5)) \
cmd.set_key ('F4', cmd.move,('x',0.5)) \
print "dialset ", dialset, " [ X ]\n" \
return dialset

def dialy(): \
global dialset \
dialset = 2 \
cmd.set_key ('F1', cmd.turn,('y',-2.0)) \
cmd.set_key ('F2', cmd.turn,('y',2.0)) \
cmd.set_key ('F3', cmd.move,('y',-0.5)) \
cmd.set_key ('F4', cmd.move,('y',0.5)) \
print "dialset ", dialset, " [ Y ]\n" \
return dialset

def dialz(): \
global dialset \
dialset = 3 \
cmd.set_key ('F1', cmd.turn,('z',-2.0)) \
cmd.set_key ('F2', cmd.turn,('z',2.0)) \
cmd.set_key ('F3', cmd.move,('z',-0.5)) \
cmd.set_key ('F4', cmd.move,('z',0.5)) \
print "dialset ", dialset, " [ Z ]\n" \
return dialset

def toggle_dial(): \
if dialset == 1 : \
print "Changing to y" \
dialy() \
elif dialset == 2 : \
print "Changing to z" \
dialz() \
elif dialset == 3 : \
print "Changing to x" \
dialx() \
else: print "Dial assignment isn't working"

cmd.set_key ('F5', toggle_dial)

# Start default dial state for rotate y (arbitrary choice)

dialy()

alias ribbonize,\
hide; show cartoon; set cartoon_fancy_helices, 1; \
hide cartoon, ( resname A or resname G or resname C or resname U or resname T ); \
show sticks, ( resname A or resname G or resname C or resname U or resname T ); \
util.rainbow; color hotpink, ( resname A or resname G or resname C or resname U or resname T )

# END COMMANDS
_ feedback pop

print "PowerMate Dial interface has been enabled"

print "Finished reading ~/.pymolrc"

</source>

← Older revision		Revision as of 19:08, 18 February 2006
Line 1:		Line 1:
		+	Here is an example of a ~/.pymolrc file that [[User:Wgscott\|I]] use on Mac OS X. There are two main things going on here:
		+
		+	* It defines a bunch of aliases, including one that ribbonizes protein/nucleic acid comples (this could benefit from updating)
		+
		+	* It runs a series of pythonized pymol commands to permit interaction with the [[MAC_Install#PowerMate_Dial \| PowerMate Dial]]
		+
		+

	<source lang="python">		<source lang="python">