Displacementmap - Revision history

Pyadmin: 7 revisions

2014-03-28T02:17:57Z

7 revisions

Tlinnet: /* References */

2012-01-15T15:03:19Z

References

Tlinnet at 23:24, 13 January 2012

2012-01-13T23:24:22Z

Tlinnet at 21:35, 11 December 2011

2011-12-11T21:35:17Z

Tlinnet at 13:06, 11 December 2011

2011-12-11T13:06:27Z

Tlinnet: /* Python Code */

2011-12-04T15:01:36Z

Python Code

Tlinnet: /* Text output */

2011-12-03T14:53:42Z

Text output

Tlinnet: /* Pymol script file */

2011-12-01T16:43:41Z

Pymol script file

Tlinnet: /* Instructions */

2011-12-01T16:42:45Z

Instructions

Tlinnet: /* Python Code */

2011-12-01T15:45:50Z

Python Code

Show changes

← Older revision		Revision as of 15:03, 15 January 2012
Line 95:		Line 95:
	[[Category:Script_Library\|DisplacementMap]]		[[Category:Script_Library\|DisplacementMap]]
	[[Category:Structural_Biology_Scripts]]		[[Category:Structural_Biology_Scripts]]
		+	[[Category:Pymol-script-repo]]

@@ Line 2: / Line 2: @@
 |type      = script
 |filename  = displacementmap.py
-|author    = [[Users:Tlinnet|Troels E. Linnet]]
+|author    = [[User:Tlinnet|Troels E. Linnet]]
 |license   = BSD
 }}

@@ Line 2: / Line 2: @@
 |type      = script
 |filename  = displacementmap.py
-|author    = Troels E. Linnet
+|author    = [[Users:Tlinnet|Troels E. Linnet]]
-|license   = Free
+|license   = BSD
 }}

@@ Line 1: / Line 1: @@
-== Author ==
+{{Infobox script-repo
-This pymol script is made by Troels Emtekær Linnet
+|type      = script
 == Overview ==
@@ Line 43: / Line 47: @@
 == Text output ==
 In the data-matrix.txt file, you find the best suggestions
-<syntaxhighlight lang="python">
+<syntaxhighlight lang="text">
 # Input 1: Open5NT  and Input 2: Closed5NT
 # Find for: CA  with min. residue-residue dist: 30.0 Angstrom
@@ Line 65: / Line 69: @@
 The script also automatically make the gnuplot plot file (.plt), with all the defined variables, for easy visualisation of the data-matrix.txt and the backbone displacement.
-== Pymol script file ==
+== Example 1 ==
-<syntaxhighlight lang="python">
+{{Template:PymolScriptRepoDownload|examples/displacementmap_1.pml}}
-import displacementmap
+<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/displacementmap_1.pml" highlight="python" />
 == References ==

@@ Line 124: / Line 124: @@
 == Python Code ==
-For a color coded view:
+{{Template:PymolScriptRepoDownload|displacementmap.py}}
 == References ==

← Older revision	Revision as of 02:17, 28 March 2014
(No difference)

@@ Line 116: / Line 116: @@
 == Pymol script file ==
 <syntaxhighlight lang="python">
-cd /homes/linnet/Documents/Speciale/5NT-project/Mutant-construct/Distance-Plot/dispmap
+import displacementmap
 fetch 1HP1, async=0
 fetch 1HPU, async=0
-−
-hide everything, all
+hide everything
 ### Select asymmetric units from pdb file
-create Open5NT, /1HP1//A
+create O5NT, /1HP1//A
-create Closed5NT, /1HPU//A
+create C5NT, /1HPU//C
 delete 1HP1
 delete 1HPU
 show cartoon, all
-set cartoon_fancy_helices=1
+super O5NT and resi 26-355, C5NT and resi 26-355
-set bg,[1,1,1]
 ### Color
 set_color goldenrod1, [1.000, 0.757, 0.145]
 color goldenrod1, resi 26-355
 set_color darkolivegreen1, [0.792, 1.000, 0.439]
-color darkolivegreen1, Open5NT and resi 356-362
+color darkolivegreen1, O5NT and resi 356-362
 set_color darkolivegreen4, [0.431, 0.545, 0.239]
-color darkolivegreen4, Closed5NT and resi 356-362
+color darkolivegreen4, C5NT and resi 356-362
 set_color chocolate3, [0.804, 0.400, 0.114]
-color chocolate3, Open5NT and resi 363-550
+color chocolate3, O5NT and resi 363-550
 set_color purple4, [0.333, 0.102, 0.545]
-color purple4, Closed5NT and resi 363-550
+color purple4, C5NT and resi 363-550
-−
 # Select active site
-select active_site, resi 117+120+252+116+217+84+41+43+254
+create active_site, resi 117+120+252+116+217+84+41+43+254
 show sticks, active_site
+disable active_site
 # Make Cys-Cys bonds
 create SS, (cys/ca+cb+sg) and byres (cys/sg and bound_to cys/sg)
 show sticks, SS
 color yellow, SS
-−
 # Mark water molecules
 create waters, resn HOH
@@ Line 175: / Line 158: @@
 color blue, waters
 disable waters
-−
 ### Make sharper, and transparent
 set fog=0
 set cartoon_transparency, 0.7
-−
 ### Load the function
 dispmap
-#dispmap Open5NT, Closed5NT, 40.0, 15.0, resi1=206, resi2=1-512.515-550
+#dispmap O5NT, C5NT, 40.0, 15.0, resi1=206, resi2=1-512.515-550
 ## Look for serine
 #dispmap mindist=40.0, mindelta=15.0, resi1=206, resi2=330.347.350.405.412.419.457.467.533.534.539.548.336.367.383.397.439.448.490.495.501.518
 #dispmap resi1=308, resi2=513
 </syntaxhighlight>

@@ Line 20: / Line 20: @@
 == Bugs ==
 If the criterion is set to low, the memory gets flooded in the data-matrix file, making the file unreadable. No solutions found yet.
 == Example ==