Pse export version - Revision history

Cchem: 1 revision

2016-10-17T00:07:04Z

1 revision

Speleo3: scenes in 1.8.4

2016-10-05T17:03:40Z

scenes in 1.8.4

Jarred at 20:28, 23 April 2015

2015-04-23T20:28:59Z

Jarred at 20:28, 23 April 2015

2015-04-23T20:28:15Z

Jarred at 20:27, 23 April 2015

2015-04-23T20:27:41Z

Jarred: Replaced content with "Find polar pairs"

2015-04-23T20:26:59Z

Replaced content with "Find polar pairs"

Jarred at 20:26, 23 April 2015

2015-04-23T20:26:18Z

Jarred at 20:16, 23 April 2015

2015-04-23T20:16:51Z

Jarred at 18:33, 22 April 2015

2015-04-22T18:33:29Z

Jarred: Reverted edits by Jarred (talk) to last revision by Bell

2015-04-22T18:09:34Z

Reverted edits by Jarred (talk) to last revision by Bell

@@ Line 21: / Line 21: @@
 The following objects are not or only partly supported:
-* scenes before 1.7.6
+* scenes before 1.7.6 (support added in 1.8.4)
 * volumes before 1.7.2
 * ramps
@@ Line 31: / Line 31: @@
 [[Category:Settings]]

@@ Line 1: / Line 1: @@
 <source lang="python">
-−
 </source>

@@ Line 1: / Line 1: @@
+<source lang="python">
-[[Category:Plugins]]
-[[Category:Biochemical_Scripts]]
+</source>

← Older revision		Revision as of 20:27, 23 April 2015
Line 1:		Line 1:
−	~~Find polar pairs~~	+
		+
		+	[[Category:Plugins]]
		+	[[Category:Biochemical_Scripts]]

← Older revision		Revision as of 20:26, 23 April 2015
Line 1:		Line 1:
−	Find polar pairs ~~with the [[find_pairs\|cmd.find_pairs]] function and return them as a list of atom pairs. It finds (more or less) the same contacts like [[distance\|cmd.distance(mode=2)]].~~	+	Find polar pairs
−
−	~~== Example ==~~
−
−	~~<source lang="python">~~
−	~~pairs = polarpairs('chain A', 'chain B')~~
−	~~for p in pairs:~~
−	~~dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])~~
−	~~print p, 'Distance: %.2f' % (dist)~~
−	~~</source>~~
−
−	~~== The Script ==~~
−
−	~~<source lang="python">~~
−	~~'''~~
−	~~(c) 2011 Thomas Holder, MPI for Developmental Biology~~
−	~~'''~~
−
−	~~from pymol import cmd~~
−
−	~~def polarpairs(sel1, sel2, cutoff=4.0, angle=63.0, name='', state=1, quiet=1):~~
−	~~'''~~
−	~~ARGUMENTS~~
−
−	~~sel1, sel2 = string: atom selections~~
−
−	~~cutoff = float: distance cutoff~~
−
−	~~angle = float: h-bond angle cutoff in degrees. If angle="default", take~~
−	~~"h_bond_max_angle" setting. If angle=0, do not detect h-bonding.~~
−
−	~~name = string: If given, also create a distance object for visual representation~~
−
−	~~SEE ALSO~~
−
−	~~cmd.find_pairs, cmd.distance~~
−	~~'''~~
−	~~cutoff = float(cutoff)~~
−	~~quiet = int(quiet)~~
−	~~state = int(state)~~
−	~~if angle == 'default':~~
−	~~angle = cmd.get('h_bond_max_angle', cmd.get_object_list(sel1)[0])~~
−	~~angle = float(angle)~~
−	~~mode = 1 if angle > 0 else 0~~
−	~~x = cmd.find_pairs('(%s) and donors' % sel1, '(%s) and acceptors' % sel2,~~
−	~~state, state,~~
−	~~cutoff=cutoff, mode=mode, angle=angle) + \~~
−	~~cmd.find_pairs('(%s) and acceptors' % sel1, '(%s) and donors' % sel2,~~
−	~~state, state,~~
−	~~cutoff=cutoff, mode=mode, angle=angle)~~
−	~~x = sorted(set(x))~~
−	~~if not quiet:~~
−	~~print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)~~
−	~~print 'Found %d polar contacts' % (len(x))~~
−	~~if len(name) > 0:~~
−	~~for p in x:~~
−	~~cmd.distance(name, '(%s`%s)' % p[0], '(%s`%s)' % p[1])~~
−	~~return x~~
−
−	~~cmd.extend('polarpairs', polarpairs)~~
−	~~</source>~~
−
−	~~[[Category:Plugins]]~~
−	~~[[Category:Biochemical_Scripts]]~~

← Older revision	Revision as of 00:07, 17 October 2016
(No difference)

@@ Line 1: / Line 1: @@
-The [[pse_export_version]] setting switches to a legacy format when saving PSEs, so far possible. The value is the floating point number representation of the targeted legacy PyMOL version, for example '''1.74''' to save a session for PyMOL 1.7.4.
+Find polar pairs with the [[find_pairs|cmd.find_pairs]] function and return them as a list of atom pairs. It finds (more or less) the same contacts like [[distance|cmd.distance(mode=2)]].
-''New in PyMOL 1.7.6''
+== Example ==
-Session file loading is always backwards compatible, so any newer version of PyMOL can load old session files.
+<source lang="python">
-== Examples ==
+== The Script ==
-<syntaxhighlight lang="python">
+<source lang="python">
-# current version (default)
+'''
-set pse_export_version, 0
+(c) 2011 Thomas Holder, MPI for Developmental Biology
-save current.pse
+'''
-# compatible with PyMOL 1.7.4
+from pymol import cmd
-== Known Limitations ==
+def polarpairs(sel1, sel2, cutoff=4.0, angle=63.0, name='', state=1, quiet=1):
-The following objects are not or only partly supported:
+    sel1, sel2 = string: atom selections
-* scenes before 1.7.6
+    cutoff = float: distance cutoff
-== See Also ==
+    angle = float: h-bond angle cutoff in degrees. If angle="default", take
-* [[save]]
+    name = string: If given, also create a distance object for visual representation
-[[Category:Settings]]
+SEE ALSO

@@ Line 6: / Line 6: @@
 == Examples ==
-<syntaxhighlighter lang="python">
 # current version (default)
 set pse_export_version, 0
@@ Line 14: / Line 15: @@
 set pse_export_version, 1.74
 save 174compat.pse
-</syntaxhighlighter>
+</syntaxhighlight>
 == Known Limitations ==