Axes - Revision history

Cchem: 1 revision

2017-03-06T06:13:40Z

1 revision

Speleo3: don't use misleading homogenous argument

2017-03-03T00:52:18Z

don't use misleading homogenous argument

Bell: 1 revision

2015-10-19T01:04:41Z

1 revision

Speleo3: fix threading issue

2015-09-29T17:34:22Z

fix threading issue

Pyadmin: 11 revisions

2014-03-28T01:31:04Z

11 revisions

New page

== Axes with text labels ==

<source lang="python">
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</source>

== Axes with nice cones ==

[[File:Axes_demo.png|300px|right]]

This script draws a simple cartesian coordinate system.

<source lang="python">
from pymol.cgo import *
from pymol import cmd

w = 0.06 # cylinder width
l = 0.75 # cylinder length
h = 0.25 # cone hight
d = w * 1.618 # cone base diameter

obj = [CYLINDER, 0.0, 0.0, 0.0, l, 0.0, 0.0, w, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0,
CYLINDER, 0.0, 0.0, 0.0, 0.0, l, 0.0, w, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0,
CYLINDER, 0.0, 0.0, 0.0, 0.0, 0.0, l, w, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0,
CONE, l, 0.0, 0.0, h+l, 0.0, 0.0, d, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0,
CONE, 0.0, l, 0.0, 0.0, h+l, 0.0, d, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0,
CONE, 0.0, 0.0, l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0]

cmd.load_cgo(obj, 'axes')
</source>

== Axes which always stay in the lower left corner ==

<source lang="python">
from pymol import cmd
from chempy import cpv

class PutCenterCallback(object):
prev_v = None

def __init__(self, name, corner=0):
self.name = name
self.corner = corner
self.cb_name = cmd.get_unused_name('_cb')

def load(self):
cmd.load_callback(self, self.cb_name)

def __call__(self):
if self.name not in cmd.get_names('objects'):
cmd.delete(self.cb_name)
return

v = cmd.get_view()
if v == self.prev_v:
return
self.prev_v = v

t = v[12:15]

if self.corner:
vp = cmd.get_viewport()
R_mc = [v[0:3], v[3:6], v[6:9]]
off_c = [0.15 * v[11] * vp[0] / vp[1], 0.15 * v[11], 0.0]
if self.corner in [2,3]:
off_c[0] *= -1
if self.corner in [3,4]:
off_c[1] *= -1
off_m = cpv.transform(R_mc, off_c)
t = cpv.add(t, off_m)

z = -v[11] / 30.0
m = [z, 0, 0, t[0] / z, 0, z, 0, t[1] / z, 0, 0, z, t[2] / z, 0, 0, 0, 1]
cmd.set_object_ttt(self.name, m, homogenous=1)

def axes(name='axes'):
'''
DESCRIPTION

Puts coordinate axes to the lower left corner of the viewport.
'''
from pymol import cgo

cmd.set('auto_zoom', 0)

w = 0.06 # cylinder width
l = 0.75 # cylinder length
h = 0.25 # cone hight
d = w * 1.618 # cone base diameter

obj = [cgo.CYLINDER, 0.0, 0.0, 0.0, l, 0.0, 0.0, w, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0,
cgo.CYLINDER, 0.0, 0.0, 0.0, 0.0, l, 0.0, w, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0,
cgo.CYLINDER, 0.0, 0.0, 0.0, 0.0, 0.0, l, w, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0,
cgo.CONE, l, 0.0, 0.0, h+l, 0.0, 0.0, d, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0,
cgo.CONE, 0.0, l, 0.0, 0.0, h+l, 0.0, d, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0,
cgo.CONE, 0.0, 0.0, l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0]

PutCenterCallback(name, 1).load()
cmd.load_cgo(obj, name)

cmd.extend('axes', axes)
</source>

[[Category:Script_Library|Axes]]
[[Category:Math_Scripts|Axes]]
[[Category:CGO]]

Speleo3: Axes which always stay in the lower left corner

2012-08-30T13:08:30Z

Axes which always stay in the lower left corner

Mretegan at 12:17, 27 March 2011

2011-03-27T12:17:32Z

Mretegan at 12:16, 27 March 2011

2011-03-27T12:16:34Z

New page

<source lang="python">
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</source>

This script draws a simple cartesian coordinate system.

<source lang="python">
from pymol.cgo import *
from pymol import cmd

w = 0.06 # cylinder width
l = 0.75 # cylinder length
h = 0.25 # cone hight
d = w * 1.618 # cone base diameter

obj = [CYLINDER, 0.0, 0.0, 0.0, l, 0.0, 0.0, w, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0,
CYLINDER, 0.0, 0.0, 0.0, 0.0, l, 0.0, w, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0,
CYLINDER, 0.0, 0.0, 0.0, 0.0, 0.0, l, w, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0,
CONE, l, 0.0, 0.0, h+l, 0.0, 0.0, d, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0,
CONE, 0.0, l, 0.0, 0.0, h+l, 0.0, d, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0,
CONE, 0.0, 0.0, l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0]

cmd.load_cgo(obj, 'axes')
</source>

Save the script and run it in Pymol. Tested in version 1.3.
[[File:Axes_demo.png|400px|left]]

[[Category:Script_Library|Axes]]
[[Category:Math_Scripts|Axes]]

Tree at 15:37, 22 February 2005

2005-02-22T15:37:52Z

Tree at 15:36, 22 February 2005

2005-02-22T15:36:57Z

← Older revision		Revision as of 15:37, 22 February 2005
Line 26:		Line 26:
	</source>		</source>

−	[[Category:~~Scripts Script Library~~\|Axes]]	+	[[Category:Scripting_Script_Library\|Axes]]

← Older revision		Revision as of 15:36, 22 February 2005
Line 26:		Line 26:
	</source>		</source>

−	[[Category:Scripts ~~Scrip~~ Library\|Axes]]	+	[[Category:Scripts Script Library\|Axes]]

← Older revision	Revision as of 06:13, 6 March 2017
(No difference)

@@ Line 95: / Line 95: @@
          z = -v[11] / 30.0
-         m = [z, 0, 0, t[0] / z, 0, z, 0, t[1] / z, 0, 0, z, t[2] / z, 0, 0, 0, 1]
+         m = [z, 0, 0, 0, 0, z, 0, 0, 0, 0, z, 0, t[0] / z, t[1] / z, t[2] / z, 1]
-         cmd.set_object_ttt(self.name, m, homogenous=1)
+         cmd.set_object_ttt(self.name, m)
 def axes(name='axes'):

← Older revision	Revision as of 01:04, 19 October 2015
(No difference)

@@ Line 72: / Line 72: @@
      def __call__(self):
          if self.name not in cmd.get_names('objects'):
-             cmd.delete(self.cb_name)
+             import threading
              return

@@ Line 1: / Line 1: @@
 <source lang="python">
 # axes.py
@@ Line 26: / Line 28: @@
 </source>
 This script draws a simple cartesian coordinate system.
@@ Line 48: / Line 53: @@
 </source>
-Save the script and run it. Tested with Pymol 1.3.
+== Axes which always stay in the lower left corner ==
-[[File:Axes_demo.png|400px|left]]
 [[Category:Script_Library|Axes]]
 [[Category:Math_Scripts|Axes]]