User:Orpheus - Revision history

Pyadmin: 14 revisions

2014-03-28T01:42:08Z

14 revisions

Orpheus: /* Code Test */

2005-02-19T22:08:42Z

Code Test

Orpheus: /* Code Test */

2005-02-19T22:06:46Z

Code Test

Orpheus: /* Code Test */

2005-02-19T22:05:19Z

Code Test

Orpheus: /* Code Test */

2005-02-19T22:03:46Z

Code Test

Orpheus: /* Code Test */

2005-02-19T22:02:29Z

Code Test

Orpheus at 21:58, 19 February 2005

2005-02-19T21:58:22Z

Orpheus: /* Graphics */

2005-02-19T21:11:41Z

Graphics

Orpheus: /* Graphics */

2005-02-18T00:13:06Z

Graphics

Orpheus at 00:12, 18 February 2005

2005-02-18T00:12:34Z

@@ Line 10: / Line 10: @@
 == Code Test ==
-−
 <source lang="python">
 from math import log

@@ Line 10: / Line 10: @@
 == Code Test ==
-−
 <source lang="python">
 from math import log

@@ Line 10: / Line 10: @@
 == Code Test ==
-−
 <source lang="python">
 from math import log

@@ Line 10: / Line 10: @@
 == Code Test ==
-−
 <source lang="python">
 from math import log

@@ Line 10: / Line 10: @@
 == Code Test ==
-−
 <source lang="python">
 from math import log

← Older revision	Revision as of 01:42, 28 March 2014
(No difference)

← Older revision		Revision as of 21:58, 19 February 2005
Line 8:		Line 8:

	[[Image:Pymolwiki.png\|PyMOL Wiki title image 1]]		[[Image:Pymolwiki.png\|PyMOL Wiki title image 1]]
		+
		+	== Code Test ==
		+
		+	<source lang="python">
		+	from math import log
		+	base = 'expt100000.1HJM_int'
		+	cmd.set('auto_zoom', 'off')
		+	cmd.set('bg_rgb', ('0', '0', '0'))
		+	cmd.set('hash_max', 240)
		+	repeat = 8 #number of frames to repeat each structure
		+
		+	for n in range(1,501):
		+	curmol = base[0:5]+str(n).zfill(5)+base[10:]
		+	# print curmol+'.pdb'
		+	cmd.load(curmol+'.pdb')
		+	if n > 1:
		+	cmd.fit(curmol+' and name ca and (resi 56 or resi 57 or resi 58)', oldmol+' and name ca and (resi 56 or resi 57 or resi 58)')
		+	cmd.delete(oldmol)
		+	# cmd.reset(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
		+	# cmd.origin(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
		+	# cmd.zoom(curmol)
		+	else:
		+	cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
		+	cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
		+	# cmd.zoom(curmol)
		+	# util.chainbow(curmol)
		+	cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)
		+	cmd.hide("lines", curmol)
		+	# cmd.show("surface", curmol)
		+	cmd.show("cartoon", curmol)
		+	# cmd.set_view ('\
		+	# 1.000000000, 0.000000000, 0.000000000,\
		+	# 0.000000000, 1.000000000, 0.000000000,\
		+	# 0.000000000, 0.000000000, 1.000000000,\
		+	# 0.000000000, 0.000000000, -717.288574219,\
		+	# 35.836936951, 12.674762726, -6.756893158,\
		+	# 565.515808105, 869.061340332, 0.000000000' )
		+	cmd.set_view('\
		+	1.000000000, 0.000000000, 0.000000000,\
		+	0.000000000, 1.000000000, 0.000000000,\
		+	0.000000000, 0.000000000, 1.000000000,\
		+	0.000000000, 0.000000000, -234.718002319,\
		+	10.384142876, 15.351722717, 11.246277809,\
		+	205.446594238, 263.989440918, 0.000000000' )
		+	cmd.translate([0,0,-0.0008nlog(n)], curmol, 0, 1, None)
		+	# cmd.zoom(curmol)
		+	cmd.clip('far', -0.5nlog(n))
		+	cmd.clip('near', -0.05nlog(n))
		+	## Uncomment one line to render frames ##
		+	# cmd.ray(1680, 1050) # 16:10 1764000
		+	# cmd.ray(1024, 576) # 16:9 589824
		+	# cmd.ray(800, 450) # 16:9 360000
		+	# cmd.ray(640, 360) # 16:9 230400
		+	# cmd.ray(480, 270) # 16:9 129600
		+	# cmd.ray(240, 180) # 16:9 43200
		+	# cmd.ray(1024, 768) # 4:3 786432
		+	cmd.ray(800, 600) # 4:3 4800000
		+	# cmd.ray(640, 480) # 4:3 307200
		+	# cmd.ray(480, 360) # 4:3 172800
		+	# cmd.ray(240, 180) # 4:3 43200
		+	## Uncomment loop to repeat frames ##
		+	for i in range(0,repeat):
		+	cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")
		+	cmd.refresh()
		+	oldmol = curmol
		+
		+	</source>

← Older revision		Revision as of 21:11, 19 February 2005
Line 6:		Line 6:
	== Graphics ==		== Graphics ==
	I'll be posting some ideas for logos and graphics for this page in the next week or so.		I'll be posting some ideas for logos and graphics for this page in the next week or so.
		+
		+	[[Image:Pymolwiki.png\|PyMOL Wiki title image 1]]

← Older revision		Revision as of 00:13, 18 February 2005
Line 6:		Line 6:
	== Graphics ==		== Graphics ==
	I'll be posting some ideas for logos and graphics for this page in the next week or so.		I'll be posting some ideas for logos and graphics for this page in the next week or so.
−
−	~~<code>~~
−	~~from math import log~~
−	~~base = 'expt100000.1HJM_int'~~
−	~~cmd.set('auto_zoom', 'off')~~
−	~~cmd.set('bg_rgb', ('0', '0', '0'))~~
−	~~cmd.set('hash_max', 240)~~
−	~~repeat = 8 #number of frames to repeat each structure~~
−
−	~~for n in range(1,501):~~
−	~~curmol = base[0:5]+str(n).zfill(5)+base[10:]~~
−	~~cmd.load(curmol+'.pdb')~~
−	~~if n > 1:~~
−	~~cmd.fit(curmol+' and name ca and (resi 56 or resi 57 or resi 58)', oldmol+' and name ca and (resi 56 or resi 57 or resi 58)')~~
−	~~cmd.delete(oldmol)~~
−	~~else:~~
−	~~cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')~~
−	~~cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')~~
−	~~cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)~~
−	~~cmd.hide("lines", curmol)~~
−	~~# cmd.show("surface", curmol)~~
−	~~cmd.show("cartoon", curmol)~~
−	~~cmd.set_view('\~~
−	~~1.000000000, 0.000000000, 0.000000000,\~~
−	~~0.000000000, 1.000000000, 0.000000000,\~~
−	~~0.000000000, 0.000000000, 1.000000000,\~~
−	~~0.000000000, 0.000000000, -234.718002319,\~~
−	~~10.384142876, 15.351722717, 11.246277809,\~~
−	~~205.446594238, 263.989440918, 0.000000000' )~~
−	~~cmd.translate([0,0,-0.0008nlog(n)], curmol, 0, 1, None)~~
−	~~cmd.clip('far', -0.5nlog(n))~~
−	~~cmd.clip('near', -0.05nlog(n))~~
−	~~## Uncomment one line to render frames ##~~
−	~~# cmd.ray(1680, 1050) # 16:10 1764000~~
−	~~# cmd.ray(1024, 576) # 16:9 589824~~
−	~~# cmd.ray(800, 450) # 16:9 360000~~
−	~~# cmd.ray(640, 360) # 16:9 230400~~
−	~~# cmd.ray(480, 270) # 16:9 129600~~
−	~~# cmd.ray(240, 180) # 16:9 43200~~
−	~~# cmd.ray(1024, 768) # 4:3 786432~~
−	~~# cmd.ray(800, 600) # 4:3 4800000~~
−	~~# cmd.ray(640, 480) # 4:3 307200~~
−	~~# cmd.ray(480, 360) # 4:3 172800~~
−	~~# cmd.ray(240, 180) # 4:3 43200~~
−	~~## Uncomment loop to repeat frames ##~~
−	~~# for i in range(0,repeat):~~
−	~~# cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")~~
−	~~cmd.refresh()~~
−	~~oldmol = curmol~~
−	~~</code>~~

← Older revision		Revision as of 00:12, 18 February 2005
Line 6:		Line 6:
	== Graphics ==		== Graphics ==
	I'll be posting some ideas for logos and graphics for this page in the next week or so.		I'll be posting some ideas for logos and graphics for this page in the next week or so.
		+
		+	<code>
		+	from math import log
		+	base = 'expt100000.1HJM_int'
		+	cmd.set('auto_zoom', 'off')
		+	cmd.set('bg_rgb', ('0', '0', '0'))
		+	cmd.set('hash_max', 240)
		+	repeat = 8 #number of frames to repeat each structure
		+
		+	for n in range(1,501):
		+	curmol = base[0:5]+str(n).zfill(5)+base[10:]
		+	cmd.load(curmol+'.pdb')
		+	if n > 1:
		+	cmd.fit(curmol+' and name ca and (resi 56 or resi 57 or resi 58)', oldmol+' and name ca and (resi 56 or resi 57 or resi 58)')
		+	cmd.delete(oldmol)
		+	else:
		+	cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
		+	cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
		+	cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)
		+	cmd.hide("lines", curmol)
		+	# cmd.show("surface", curmol)
		+	cmd.show("cartoon", curmol)
		+	cmd.set_view('\
		+	1.000000000, 0.000000000, 0.000000000,\
		+	0.000000000, 1.000000000, 0.000000000,\
		+	0.000000000, 0.000000000, 1.000000000,\
		+	0.000000000, 0.000000000, -234.718002319,\
		+	10.384142876, 15.351722717, 11.246277809,\
		+	205.446594238, 263.989440918, 0.000000000' )
		+	cmd.translate([0,0,-0.0008nlog(n)], curmol, 0, 1, None)
		+	cmd.clip('far', -0.5nlog(n))
		+	cmd.clip('near', -0.05nlog(n))
		+	## Uncomment one line to render frames ##
		+	# cmd.ray(1680, 1050) # 16:10 1764000
		+	# cmd.ray(1024, 576) # 16:9 589824
		+	# cmd.ray(800, 450) # 16:9 360000
		+	# cmd.ray(640, 360) # 16:9 230400
		+	# cmd.ray(480, 270) # 16:9 129600
		+	# cmd.ray(240, 180) # 16:9 43200
		+	# cmd.ray(1024, 768) # 4:3 786432
		+	# cmd.ray(800, 600) # 4:3 4800000
		+	# cmd.ray(640, 480) # 4:3 307200
		+	# cmd.ray(480, 360) # 4:3 172800
		+	# cmd.ray(240, 180) # 4:3 43200
		+	## Uncomment loop to repeat frames ##
		+	# for i in range(0,repeat):
		+	# cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")
		+	cmd.refresh()
		+	oldmol = curmol
		+	</code>