Selections:

Selections force spock commands to apply to only a subset of atoms or vertices. Unlike some graphics packages, spock selections apply only to the current command; they are not persistent. In the descriptions below, RANGE indicates an inclusive range, e.g. rn=(1,10), where all items in the inclusive range are selected. LIST indicates listed entries, e.g. rn=[2,4,5,9], where only the items in the list are selected. Finally, NUMBER indicates a single value, e.g. rn=5, where only items matching that number are selected.

The following relationships may be used in a selection string: ``='' (equals), ``<>'' (not equals), ``>'' (greater than), ``<'' (less than), ``>= or =>'' (greater than or equals) and ``<= or =<'' (less than or equals). These relationships may be applied to NUMBERS. For RANGEs and LISTs only ``='' and ``<>'' are valid, e.g. rn<>[1,2,3],an=(1,2). Finally, for strings, only the ``='' and ``<>'' relations are valid.

• Object number
  • vn=<RANGE,LIST,NUMBER> (vertex number)
  • s=<RANGE,LIST,NUMBER> (surface number)
  • hn=<RANGE,LIST,NUMBER> (helix number)
  • sn=<RANGE,LIST,NUMBER> (sheet number)
  • tn=<RANGE,LIST,NUMBER> (sheet number)
  • nn=<RANGE,LIST,NUMBER> (note number)
  • in=<RANGE,LIST,NUMBER> (interaction number)
  • m=<RANGE,LIST,NUMBER> (molecule number)
  • model=<RANGE,LIST,NUMBER> (molecule number)
• Identity
  • rn=<RANGE,LIST,NUMBER> (residue number)
  • an=<RANGE,LIST,NUMBER> (internal atom number)
  • pdban=<RANGE,LIST,NUMBER> (pdb atom number)
  • element=<RANGE,LIST,NUMBER> (element number or 0 for CA)
  • a=<NAME|ba|sch>, (atom name, backbone or side chain)
  • r=<NAME|property>, (select on residue name or property. Valid properties are: substrate, aliphatic, hydroxyl, sulfur, aromatic, charged, amide, hydrophobic, polar, neutral, acidic, basic, small, medium, large, cyclic, dna, aa, at, cg, purine, pyrimidine, wat, helix, sheet, turn, and coil.)
  • ch=L, (chain name)
  • sub=<NAME|NUMBER>, (atom subset name or number)
  • vsub=<NAME|NUMBER>, (surface subset name or number)
  • altloc=L, (alternate location identifier)
  • icode=L, (insertion code identifier)
• Atom Property
  • q=<RANGE|LIST|NUMBER>, (atom charge)
  • d=<RANGE|LIST|NUMBER>, (atom distance)
  • dp=<RANGE|LIST|NUMBER>, (atom distance partner)
  • sa=<RANGE|LIST|NUMBER>, (surface area)
  • p=<RANGE|LIST|NUMBER>, (potential area)
  • ap1=<RANGE|LIST|NUMBER>, (atom property 1)
  • ap2=<RANGE|LIST|NUMBER>, (atom property 2)
  • radius=<RANGE|LIST|NUMBER>, (atom radius)
  • x/y/z=<RANGE|LIST|NUMBER>, (untransformed atom coordinate)
  • X/Y/Z=<RANGE|LIST|NUMBER>, (transformed/screen atom coordinate)
  • iv=<RANGE|LIST|NUMBER>, (interaction intensity value)
  • it=<RANGE|LIST|NUMBER>, (interaction tpye)
  • ip=1, or ip=-1, (most positive or most negative interaction)
• Color
  • ac=<RANGE|LIST|NUMBER>, (atom color)
  • bc=<RANGE|LIST|NUMBER>, (bond color)
  • wc=<RANGE|LIST|NUMBER>, (worm color)
  • lc=<RANGE|LIST|NUMBER>, (label color)
• Vertex Property
  • vc=<RANGE|LIST|NUMBER>, (vertex color)
  • vd=<RANGE|LIST|NUMBER>, (vertex distance)
  • vp1=<RANGE|LIST|NUMBER>, (vertex property 1)
  • vp2=<RANGE|LIST|NUMBER>, (vertex property 2)
  • vp=<RANGE|LIST|NUMBER>, (vertex potential)
  • vx/vy/vz=<RANGE|LIST|NUMBER>, (untransformed vertex coordinate)
  • vX/vY/vZ=<RANGE|LIST|NUMBER> (transformed/screen vertex coordinate)
• Bonding
  • bcnt=<RANGE,LIST,NUMBER> (number of bonds)
  • hbcnt=<RANGE,LIST,NUMBER> (number of H-bonds)
  • hbond (if atom is hbonded to it's distance partner)