Editing User:Speleo3 (section)

=== 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>