Renumber - Revision history

Bell: 6 revisions

2014-03-28T03:49:13Z

6 revisions

Speleo3: recursion limit

2012-06-16T10:27:07Z

recursion limit

Speleo3: fuse example

2012-06-13T11:14:08Z

fuse example

Tlinnet at 14:00, 9 February 2012

2012-02-09T14:00:21Z

Speleo3: moved script to github

2012-02-01T09:44:59Z

moved script to github

Speleo3: created

2012-01-31T10:31:37Z

created

Slaw: Redirected page to Pdb retain ids

2009-05-19T17:38:15Z

Redirected page to Pdb retain ids

New page

#REDIRECT [[pdb retain ids]]

@@ Line 34: / Line 34: @@
 renumber chain2
 sort chain2
 </syntaxhighlight>

@@ Line 20: / Line 20: @@
 # renumber polymer, first 27 residues of Q8N2U3_HUMAN missing.
 renumber chain A, 28
 </syntaxhighlight>

← Older revision		Revision as of 14:00, 9 February 2012
Line 29:		Line 29:

	[[Category:Script_Library]]		[[Category:Script_Library]]
		+	[[Category:Pymol-script-repo]]

@@ Line 1: / Line 1: @@
 [[renumber]] sets new residue numbers (resi) for a polymer based on connectivity.
@@ Line 13: / Line 20: @@
 # renumber polymer, first 27 residues of Q8N2U3_HUMAN missing.
 renumber chain A, 28
 </syntaxhighlight>

← Older revision		Revision as of 10:31, 31 January 2012
Line 1:		Line 1:
−	#~~REDIRECT~~ [[~~pdb retain ids~~]]	+	[[renumber]] sets new residue numbers (resi) for a polymer based on connectivity.
		+
		+	== Example ==
		+
		+	This examples takes a pdb structure with insertion codes and sets a new, linear numbering based on [http://www.uniprot.org/uniprot/Q8N2U3_HUMAN Q8N2U3_HUMAN].
		+
		+	<syntaxhighlight lang="python">
		+	fetch 1h4w, async=0
		+
		+	# move everything which is not polymer to another chain
		+	alter not polymer, chain="B"
		+
		+	# renumber polymer, first 27 residues of Q8N2U3_HUMAN missing.
		+	renumber chain A, 28
		+	</syntaxhighlight>
		+
		+	== The Script ==
		+
		+	<syntaxhighlight lang="python">
		+	from pymol import cmd, CmdException
		+
		+	def renumber(selection='all', start=1, startsele=None, quiet=1):
		+	'''
		+	DESCRIPTION
		+
		+	Set residue numbering (resi) based on connectivity.
		+
		+	ARGUMENTS
		+
		+	selection = string: atom selection to renumber {default: all}
		+
		+	start = integer: counting start {default: 1}
		+
		+	startsele = string: residue to start counting from {default: first in
		+	selection}
		+	'''
		+	start, quiet = int(start), int(quiet)
		+	model = cmd.get_model(selection)
		+	cmd.iterate(selection, 'atom_it.next().model = model',
		+	space={'atom_it': iter(model.atom)})
		+	if startsele is not None:
		+	startidx = cmd.index('first (' + startsele + ')')[0]
		+	for atom in model.atom:
		+	if (atom.model, atom.index) == startidx:
		+	startatom = atom
		+	break
		+	else:
		+	print ' Error: startsele not in selection'
		+	raise CmdException
		+	else:
		+	startatom = model.atom[0]
		+	for atom in model.atom:
		+	atom.adjacent = []
		+	atom.visited = False
		+	for bond in model.bond:
		+	atoms = [model.atom[i] for i in bond.index]
		+	atoms[0].adjacent.append(atoms[1])
		+	atoms[1].adjacent.append(atoms[0])
		+	def traverse(atom, resi):
		+	atom.resi = resi
		+	atom.visited = True
		+	for other in atom.adjacent:
		+	if other.visited:
		+	continue
		+	if (atom.name, other.name) in [('C','N'), ("O3'", 'P')]:
		+	traverse(other, resi+1)
		+	elif (atom.name, other.name) in [('N','C'), ('P', "O3'")]:
		+	traverse(other, resi-1)
		+	elif (atom.name, other.name) not in [('SG', 'SG')]:
		+	traverse(other, resi)
		+	traverse(startatom, start)
		+	cmd.alter(selection, 'resi = atom_it.next().resi',
		+	space={'atom_it': iter(model.atom)})
		+
		+	cmd.extend('renumber', renumber)
		+
		+	# vi:expandtab:smarttab
		+	</syntaxhighlight>
		+
		+	== See Also ==
		+
		+	* [[alter]]
		+	* [[rename]]
		+	* [[pdb_retain_ids]]
		+
		+	[[Category:Script_Library]]

← Older revision	Revision as of 03:49, 28 March 2014
(No difference)