Web Services - Sample 01: API Documentation & Validation

Please click the link(s) below before testing methods in this section (in order).

    /apply/pymol.cmd.reinitialize

- load filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial

      /apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb

      /apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4

- enable name, parents

      /apply/pymol.cmd.enable?name=map

- disable name

      /apply/pymol.cmd.disable?name=map

- get_names type, enabled_only, selection

      /apply/pymol.cmd.get_names

      /apply/pymol.cmd.get_names?enabled_only=1

- delete name

      /apply/pymol.cmd.delete?name=ref

- reinitialize what, object

      /apply/pymol.cmd.reinitialize

Please click the link(s) below before testing methods in this section (in order).

    /apply/pymol.cmd.reinitialize

    /apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb

- color color, selection, quiet, flags

      /apply/pymol.cmd.color?color=yellow&selection=elem c

      /apply/pymol.cmd.color?color=cyan&selection=elem c

- center selection, state, origin, animate

      /apply/pymol.cmd.center?selection=polymer and resi 61

- zoom selection, buffer, state, complete, animate

      /apply/pymol.cmd.zoom?selection=byres 50/ca&animate=1

- reset object

      /apply/pymol.cmd.reset

- clip mode, distance, selection, state

      /apply/pymol.cmd.clip?mode=slab&distance=10

      /apply/pymol.cmd.clip?mode=move&distance=5

      /apply/pymol.cmd.clip?mode=atoms&distance=2&selection=all

- orient selection, state, animate

      /apply/pymol.cmd.orient?selection=ref&animate=2

- set_view view, animate, quiet, hand

      /apply/pymol.cmd.set_view?view=[0.578752935,0.681042910,0.448581249,-0.788007200,0.608662128,0.092595495,-0.209973529,-0.407075256,0.888932705,0.000007167,-0.000031501,-51.499031067,32.479228973,33.349739075,16.644239426,43.353927612,59.644340515,-20.000000000]&animate=2

- get_view output, quiet

      /apply/pymol.cmd.get_view

Please click the link(s) below before testing methods in this section (in order).

    /apply/pymol.cmd.reinitialize

    /apply/pymol.cmd.load?filename=$PYMOL_PATH/test/dat/pept.pdb

- distance name, selection1, selection2, cutoff, mode, zoom, width, length, gap, label, quiet, reset, state

      /apply/pymol.cmd.distance?name=trp2trp&selection1=/pept/E/E/TRP`4/CD2&selection2=/pept/E/E/TRP`11/CD2

      /apply/pymol.cmd.distance?name=hbonds&selection1=pept&selection2=pept&mode=2&label=0

      /apply/pymol.cmd.show?representation=labels&selection=hbonds

      /apply/pymol.cmd.hide?representation=labels&selection=hbonds

- angle name, selection1, selection2, selection3, mode, label, reset, zoom, state, quiet

      /apply/pymol.cmd.angle?name=gly-angs&selection1=gly/&selection2=gly/&selection3=gly/&mode=1

      /apply/pymol.cmd.zoom?selection=gly-angs&animate=1

- dihedral name, selection1, selection2, selection3, selection4, mode, label, reset, zoom, state, quiet

      /apply/pymol.cmd.dihedral?name=leu-dihe&selection1=6/N&selection2=6/CA&selection3=6/C&selection4=6/O

      /apply/pymol.cmd.zoom?selection=leu-dihe&animate=1

- get_distance atom1, atom2, state, quiet

      /apply/pymol.cmd.get_distance?atom1=1/CA&atom2=2/CA

- get_angle atom1, atom2, atom3, state, quiet

      /apply/pymol.cmd.get_angle?atom1=1/N&atom2=1/CA&atom3=1/C

- get_dihedral atom1, atom2, atom3, atom4, state, quiet

      /apply/pymol.cmd.get_dihedral?atom1=1/N&atom2=1/CA&atom3=1/C&atom4=2/N

Please click the link(s) below before testing methods in this section (in order).

    /apply/pymol.cmd.reinitialize

    /apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb

    /apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4

- isomesh name, map, level, selection, buffer, state, carve, source_state, quiet

      /apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0

      /apply/pymol.cmd.rock

- isolevel name, level, state, query, quiet

      /apply/pymol.cmd.isolevel?name=mesh&level=3.0

      /apply/pymol.cmd.isolevel?name=mesh&level=-2.0

- isosurface name, map, level, selection, buffer, state, carve, source_state, side, mode, quiet

      /apply/pymol.cmd.isosurface?name=surf&map=map&level=5.0

      /apply/pymol.cmd.color?color=red&selection=surf

Please click the link(s) below before testing methods in this section (in order).

    /apply/pymol.cmd.reinitialize

    /apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb

- show representation, selection

      /apply/pymol.cmd.show?representation=sticks

- hide representation, selection

      /apply/pymol.cmd.hide?representation=nonbonded

- set name, value, selection, state, updates, log, quiet

      /apply/pymol.cmd.set?name=stick_radius&value=0.4

      /apply/pymol.cmd.set?name=stick_radius&value=0.15

- get name, selection, state, quiet

      /apply/pymol.cmd.get?name=stick_radius

- label selection, expression, quiet

      /apply/pymol.cmd.label?selection=resn sul and elem s&expression='Sulfate'

      /apply/pymol.cmd.label?selection=name ca&expression=chain+' '+resi+' '+resn

      /apply/pymol.cmd.label?selection=visible&expression=name

      /apply/pymol.cmd.label?selection=all&expression=

Please click the link(s) below before testing methods in this section (in order).

    /apply/pymol.cmd.reinitialize

    /apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb

- show_as representation, selection

      /apply/pymol.cmd.show_as?representation=spheres

- draw width, height, antialias, quiet

      /apply/pymol.cmd.draw?width=1024

- ray width, height, antialias, angle, shift, renderer, quiet, async

      /apply/pymol.cmd.ray?async=1

Please click the link(s) below before testing methods in this section (in order).

    /apply/pymol.cmd.reinitialize

    /apply/pymol.cmd.load?filename=$PYMOL_PATH/test/dat/pept.pdb

- select name, selection, enable, quiet, merge, state, domain

      /apply/pymol.cmd.select?name=mysel1&selection=1-2/&enable=1

      /apply/pymol.cmd.show?representation=spheres&selection=mysel1

- origin selection, object, position, state

      /apply/pymol.cmd.origin?selection=mysel1

      /apply/pymol.cmd.turn?axis=x&angle=45

Please click the link(s) below before testing methods in this section (in order).

    /apply/pymol.cmd.reinitialize

    /apply/pymol.cmd.load?filename=$TUT/1hpv.pdb

- create name, selection, source_state, target_state, discrete, zoom, quiet, singletons, extract

      /apply/pymol.cmd.create?name=chA&selection=chain A

      /apply/pymol.cmd.create?name=chB&selection=chain B

      /apply/pymol.cmd.delete?name=1hpv

      /apply/pymol.cmd.orient

- align mobile, target, cutoff, cycles, gap, extend, max_gap, object, matrix, mobile_state, target_state, quiet, max_skip, transform, reset

      /apply/pymol.cmd.align?mobile=chA&target=chB

Please click the link(s) below before testing methods in this section (in order).

    /apply/pymol.cmd.reinitialize

    /apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb

- super mobile, target, cutoff, cycles, gap, extend, max_gap, object, matrix, mobile_state, target_state, quiet, max_skip, transform, reset, seq, radius, scale, base, coord, expect, window, ante

      /apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/

      /apply/pymol.cmd.create?name=helix2&selection=polymer and 42-60/

      /apply/pymol.cmd.delete?name=ref

      /apply/pymol.cmd.orient

      /apply/pymol.cmd.super?mobile=helix1////CA&target=helix2////CA

- window action, x, y, width, height

      /apply/pymol.cmd.window?action=position&x=200&y=300

      /apply/pymol.cmd.window?action=position&x=0&y=100

      /apply/pymol.cmd.window?action=size&x=600&y=600

      /apply/pymol.cmd.window?action=size&x=800&y=700