General Pymol Utilities

show axes, transform things, etc.

pymol_util.inpymol()

pymol_util.rainbow_chains()

pymol_util.showaxes()

class pymol_util.PutCenterCallback(name, corner=0)

prev_v = None

load()

pymol_util.corneraxes(name='axes')

DESCRIPTION

Puts coordinate axes to the lower left corner of the viewport.

pymol_util.showaxes2()

pymol_util.getchain(sele)

pymol_util.getres(sele, withchain=True)

pymol_util.getrestypes(sele)

pymol_util.com(sel='all', state=1)

pymol_util.showcom(sel='all')

pymol_util.cgo_sphere(c, r=1, col=(1, 1, 1))

pymol_util.showsphere(c, r=1, col=(1, 1, 1), lbl='')

pymol_util.showvecfrompoint(a, c, col=(1, 1, 1), lbl='')

pymol_util.cgo_segment(c1, c2, col=(1, 1, 1))

pymol_util.showsegment(c1, c2, col=(1, 1, 1), lbl='')

pymol_util.cgo_cyl(c1, c2, r, col=(1, 1, 1), col2=None)

pymol_util.showcyl(c1, c2, r, col=(1, 1, 1), col2=None, lbl='')

pymol_util.showline(a, c, col=(1, 1, 1), lbl='')

pymol_util.cgo_lineabs(a, c, col=(1, 1, 1))

pymol_util.showlineabs(a, c, col=(1, 1, 1), lbl='')

class pymol_util.ResBB(n, ca=None, c=None, ss=None)

docstring for ResBB

rms(s, o)

stub(r)

class pymol_util.DisulfLib(fn)

docstring for DisulfLib

disulf_rms(r1, r2)

pymol_util.chirality(fe1, fe2, fe3, fe4)

pymol_util.bond_zns(sel)

pymol_util.trans(sel, v)

pymol_util.transx(sel, x)

pymol_util.transy(sel, y)

pymol_util.transz(sel, z)

pymol_util.rot(sel, axis, ang, cen=Vec( 0.000000, 0.000000, 0.000000 ))

pymol_util.rotx(sel, ang, cen=Vec( 0.000000, 0.000000, 0.000000 ))

pymol_util.roty(sel, ang, cen=Vec( 0.000000, 0.000000, 0.000000 ))

pymol_util.rotz(sel, ang, cen=Vec( 0.000000, 0.000000, 0.000000 ))

pymol_util.xform(sel, x)

pymol_util.rot_by_matrix(sel, R, cen=Vec( 0.000000, 0.000000, 0.000000 ))

pymol_util.rotrad(sel, axis, ang, cen=None)

pymol_util.test(x, y, z)

pymol_util.rotview(axis, ang, cen=Vec( 0.000000, 0.000000, 0.000000 ))

pymol_util.pointaxis(sel)

pymol_util.alignaxis(sel, newaxis, oldaxis=None, cen=Vec( 0.000000, 0.000000, 0.000000 ))

pymol_util.mysetview(look=Vec( 0.000000, 0.000000, 1.000000 ), up=Vec( 0.000000, 1.000000, 0.000000 ), pos=None, cen=None, ncp=None, fcp=None)

pymol_util.meancoords(sel1, sel2, n='mix', w=0.5)

pymol_util.mygetview()

pymol_util.swell()

pymol_util.mkhelix(sel, t, r, n)

pymol_util.mkhelix4(sel, t, r, n)

pymol_util.mirror(sel, nname='mirror', crd=0)

pymol_util.inversion(sel, nname='inv')

pymol_util.mkc4(sel, a=Vec( 1.000000, 0.000000, 0.000000 ), c=Vec( 0.000000, 0.000000, 0.000000 ))

pymol_util.mkc3(sel, a=Vec( 0.000000, 0.000000, 1.000000 ), c=Vec( 0.000000, 0.000000, 0.000000 ))

pymol_util.mkc2(sel, a=Vec( 0.000000, 0.000000, 1.000000 ), c=Vec( 0.000000, 0.000000, 0.000000 ))

pymol_util.mkd2(sel='all')

pymol_util.alignbb(sel='all', obj=None)

pymol_util.alignall(sel='all', obj=None)

pymol_util.fitall(sel='all', obj=None)

pymol_util.centerall(sel='all')

pymol_util.showcst(fname)

pymol_util.bondzn()

pymol_util.loadmov(d)

pymol_util.drawlines(p, d, lab='lines', COL=(1, 1, 1), SIZE=20.0)

pymol_util.drawtestconeva(v, a)

pymol_util.conelineinter(p, d, v, a, t)

pymol_util.createpoint(sele, p, lab)

pymol_util.test_conelineinter(sele)

pymol_util.useRosettaRadii()

pymol_util.expandRadii(delta=1.0, sel='all')

pymol_util.contractRadii(delta=1.0, sel='all')

pymol_util.useOccColors(sel='all')

pymol_util.useTempColors(sel='all')

pymol_util.useOccRadii(sel='all')

pymol_util.useTempRadii(sel='all')

pymol_util.natom(sel='all')

pymol_util.nca(sel='all')

pymol_util.chaincount(sel='all')

pymol_util.getname1(s)

pymol_util.lcs(S, T)

pymol_util.sort_dcoms(subs)

pymol_util.procD5dat(lfile=None, biod='/data/biounit', outd=None)

pymol_util.untangle_sidechains(sele)

pymol_util.orb_cyl(lab='')

pymol_util.drawring(p1=None, p2=None, p3=None, col=[1, 1, 1], lab='ring')

pymol_util.drawringcar(c, a, r, col=[1, 1, 1], lab='ring')

pymol_util.drawsph(col=[1, 1, 1], lab='sph')

pymol_util.dsf(CA1, CB1, CA2, CB2, lab='')

pymol_util.alignallrms(sele)

pymol_util.mkpntx(s1, s2)

pymol_util.ifsphab()

pymol_util.charge(sel)

pymol_util.redoA(sel='not sub', N=None)

pymol_util.redotoi(sel='not sub*')

pymol_util.redopent(sel)

pymol_util.getaa(c, r, o='all')

pymol_util.mkifaceresfile(fn=None)

pymol_util.color_by_chain()

pymol_util.getnative()

pymol_util.floats2vecs(i)

pymol_util.nnb(v, s, r)

pymol_util.testhsphere(rratio=2.0)

pymol_util.testsphere()

pymol_util.stubalign(s='all', s1='pk1', s2='pk2', s3='pk3')

pymol_util.tmpdoit()

pymol_util.symmetrizec2(sel1, sel2)

pymol_util.corresponding_atom_names(sel1, sel2, file)

pymol_util.bestalign(s1, s2)

pymol_util.process_native()

pymol_util.move_up_down_add_to_ignore_list(sel)

pymol_util.my_get_obj(enabled_only=0)

pymol_util.move_down()

pymol_util.move_up()

pymol_util.cbow(sel='all')

pymol_util.print_chains(sele='all')

pymol_util.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}

pymol_util.color_obj(rainbow=0)

AUTHOR

Gareth Stockwell

USAGE

color_obj(rainbow=0)

This function colours each object currently in the PyMOL heirarchy with a different colour. Colours used are either the 22 named colours used by PyMOL (in which case the 23rd object, if it exists, gets the same colour as the first), or are the colours of the rainbow

SEE ALSO

util.color_objs()

pymol_util.tcdock_set_chain_by_cluster()

pymol_util.hsv_to_rgb(hsv)

pymol_util.make_zdock_set(d='/work/sheffler/Dropbox/project/zdock/pdb_lib', tgt='/work/sheffler/data/zdock_AB')

pymol_util.make_inputs_from_cb_only(d='/work/sheffler/Dropbox/test/silva/run_resl_6/', tgt='/work/sheffler/tmp/asym_iface')

pymol_util.get_closest_atom_pair(selpairs_or_sel1, sel2=None)

pymol_util.get_first_last_resi(sele)

pymol_util.cube(lb=Vec( -10.000000, -10.000000, -10.000000 ), ub=Vec( 10.000000, 10.000000, 10.000000 ), r=0.5, xform=Xform( Mat( Vec( 1.000000, 0.000000, 0.000000 ), Vec( 0.000000, 1.000000, 0.000000 ), Vec( 0.000000, 0.000000, 1.000000 ) ), Vec( 0.000000, 0.000000, 0.000000 ) ))

pymol_util.getframe(obj)

pymol_util.getrelframe(newobj, refobj, Forigin=None)

get transform between two objects, assume the obj’s are identical

pymol_util.getrelframe_rmsalign(movsel, refsel, Forigin=None)

get transform between two objects using rmsalign

pymol_util.tmpvis(s)

pymol_util.show_res_frames(sele)