User:Speleo3 - Revision history

Cchem: 1 revision

2018-01-08T04:03:37Z

1 revision

Speleo3: FreeBSD

2017-12-16T18:20:23Z

FreeBSD

Cchem: 1 revision

2017-02-06T03:04:57Z

1 revision

Speleo3: ligand_zoom

2017-01-27T23:17:06Z

ligand_zoom

Cchem: 1 revision

2016-12-12T03:26:20Z

1 revision

Speleo3: interactive ipython terminal

2016-11-16T23:13:51Z

interactive ipython terminal

Cchem: 1 revision

2016-06-27T02:04:50Z

1 revision

Speleo3: transparent movie

2016-06-14T21:37:45Z

transparent movie

Bell: 1 revision

2016-03-07T03:47:42Z

1 revision

Speleo3: ccmutate

2016-02-19T19:44:13Z

ccmutate

@@ Line 41: / Line 41: @@
      _COb = pymol._cmd._new(pymol, pymol.invocation.options)
      pymol._cmd._start(_COb, pymol.cmd)
 from pymol import cmd
@@ Line 385: / Line 386: @@
      cmd.do('zoom /%s/%s/%s & resi %s, animate=1, buffer=2' % ligands[i])
 </source>

@@ Line 363: / Line 363: @@
          cmd.delete(tmp_sc_o)
          cmd.delete(tmp_sc_n)
 </source>

@@ Line 29: / Line 29: @@
 Launch interactive python terminal with PyMOL process:
 (see also [[Launching From a Script]])
 <source lang="python">

@@ Line 50: / Line 50: @@
 pymol.finish_launching()
 cmd = pymol.cmd
 </source>
@@ Line 175: / Line 145: @@
 $MENCODER "$pattern" $MPEG1ARGS:vpass=1 -o /dev/null
 $MENCODER "$pattern" $MPEG1ARGS:vpass=2 -o "$outfile"
 </source>

← Older revision		Revision as of 19:44, 19 February 2016
Line 246:		Line 246:

	shutil.rmtree(outdir)		shutil.rmtree(outdir)
		+	</source>
		+
		+	=== ccmutate ===
		+
		+	<source lang="python">
		+	@cmd.extend
		+	def ccmutate(code, selection='??sele\|?pk1', sculpt=1):
		+	'''
		+	DESCRIPTION
		+
		+	Mutate selected residue.
		+
		+	ARGUMENTS
		+
		+	code = str: 3-letter PDBeChem chemical component identifier
		+
		+	selection = str: single residue selection {default: pk1 or sele}
		+
		+	sculpt = 0/1: try to adopt conformation of replaced sidechain, followed
		+	by relaxation using sculpting {default: 1}
		+
		+	EXAMPLE
		+
		+	fetch 1ubq, async=0
		+	ccmutate 0HG, resi 24
		+
		+	SEE ALSO
		+
		+	fetch ..., type=cc
		+	wizard mutagenesis
		+	'''
		+	code = code.upper()
		+
		+	tmp_sele = cmd.get_unused_name('_sele')
		+	tmp_frag = cmd.get_unused_name('_frag')
		+	tmp_Nnbr = cmd.get_unused_name('_Nnbr')
		+	tmp_back = cmd.get_unused_name('_back')
		+	tmp_tmpl = cmd.get_unused_name('_tmpl')
		+	tmp_sc_o = cmd.get_unused_name('_sc_o')
		+	tmp_sc_n = cmd.get_unused_name('_sc_n')
		+
		+	try:
		+	cmd.select(tmp_sele, 'byres (' + selection + ')', 0)
		+
		+	# check input selection
		+	if cmd.count_atoms('name CA & ?' + tmp_sele) != 1:
		+	raise pymol.CmdException('selection must include exactly one residue')
		+	if cmd.count_atoms('name N+CA+C & ?' + tmp_sele) != 3:
		+	raise pymol.CmdException("selected residue doesn't have N+CA+C atoms")
		+
		+	# PDBeChem fragment
		+	cmd.fetch(code, tmp_frag, type='cc', zoom=0)
		+
		+	# check if fragment is amino acid
		+	if cmd.count_atoms('name N+CA+C & ?' + tmp_frag) != 3:
		+	raise pymol.CmdException("residue '%s' doesn't have N+CA+C atoms" % (code))
		+
		+	# only keep hydrogens if target also has hydrogens
		+	if cmd.count_atoms('hydro & ?' + tmp_sele) == 0:
		+	cmd.remove('hydro & ?' + tmp_frag)
		+
		+	# update residue name for old residue
		+	cmd.alter(tmp_sele, 'resn = ' + repr(code))
		+
		+	# superpose fragment on backbone
		+	cmd.align(
		+	'name N+CA+C & ?' + tmp_frag,
		+	'name N+CA+C & ?' + tmp_sele)
		+
		+	# extra N bonds, like in PRO
		+	cmd.select(tmp_Nnbr, 'neighbor (name N & ?' + tmp_frag + ')', 0)
		+
		+	# backbone selection
		+	cmd.select(tmp_back, 'name CA+C+O+N+OXT', 0)
		+	cmd.select(tmp_back, 'hydro & neighbor ?' + tmp_back, 0, merge=1)
		+
		+	# remove complementary atoms
		+	cmd.remove( '?' + tmp_frag + ' & ' + tmp_back)
		+	cmd.extract(tmp_tmpl, '?' + tmp_sele + ' & !' + tmp_back, zoom=0)
		+
		+	if cmd.count_atoms(tmp_frag):
		+	# attach new sidechain
		+	cmd.fuse('name CB & ?' + tmp_frag, 'name CA & ?' + tmp_sele, mode=1, move=0)
		+	cmd.unpick()
		+
		+	# new atom selections
		+	cmd.select(tmp_sc_n, '(byres ?' + tmp_sele + ') & !?' + tmp_sele, 0)
		+	cmd.select(tmp_sc_o, '?' + tmp_sc_n + ' like ?' + tmp_tmpl, 0)
		+
		+	# extra N bonds, like in PRO
		+	if cmd.count_atoms(tmp_Nnbr):
		+	cmd.bond('?' + tmp_sc_n + ' like ?' + tmp_Nnbr, 'name N & ?' + tmp_sele)
		+
		+	# adopt old conformation, if possible
		+	if int(sculpt):
		+	model = cmd.get_object_list('?' + tmp_sele)[0]
		+	cmd.protect(model)
		+	cmd.deprotect('?' + tmp_sc_n + ' & !?' + tmp_sc_o)
		+	cmd.sculpt_activate(model)
		+	if cmd.count_atoms(tmp_sc_o):
		+	cmd.update(tmp_sc_o, tmp_tmpl)
		+	cmd.set('sculpt_field_mask', 63) # local geom + vdw
		+	cmd.sculpt_iterate(model, cycles=100)
		+	cmd.deprotect(tmp_sc_o)
		+	cmd.set('sculpt_field_mask', 0xff) # all
		+	cmd.sculpt_iterate(model, cycles=200)
		+	cmd.set('sculpt_field_mask', 31) # local geom
		+	cmd.sculpt_iterate(model, cycles=200)
		+
		+	finally:
		+	cmd.delete(tmp_sele)
		+	cmd.delete(tmp_frag)
		+	cmd.delete(tmp_Nnbr)
		+	cmd.delete(tmp_back)
		+	cmd.delete(tmp_tmpl)
		+	cmd.delete(tmp_sc_o)
		+	cmd.delete(tmp_sc_n)
	</source>		</source>

← Older revision	Revision as of 04:03, 8 January 2018
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← Older revision	Revision as of 03:04, 6 February 2017
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← Older revision	Revision as of 03:26, 12 December 2016
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← Older revision	Revision as of 02:04, 27 June 2016
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← Older revision	Revision as of 03:47, 7 March 2016
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