Segn  PROA

All atoms in segment “PROA”

Residue PROA 11

All atoms of residue 11 in segment “PROA”

Atom PROA 11 C

Atom “C” in residue 11 in segment “PROA”

all

Means whole system, no arguments needed

none

Means nothing, no arguments needed

hydrogen

All Hydrogen atoms

heavyAtom

All atoms except hydrogen, no arguments needed

noCoord

All atoms with unknown coordinates, no arguments needed

name

All atoms in the name lists enumerated.

Example:

  defgroup mainchain Select=”name C N O CA”

  defgroup carbons select=”name C*”

resn

All atoms in residue name lists enumerated.

Example:

  defGroup phes Select=”resn PHE”

  defgroup pheiles select=”resn PHE ILE”

iseg

All atoms in index number i segment. the index start from 0;

  Defgroup seg0  select=”iseg 0”

ires

All atoms in index number i residue

defgroup proa select=”segn PROA”

  defgroup res1  select=”ires 1 in PROA”

segn, or seg

All atoms in segment name lists enumerated.

  defgroup proa select=”segn PROA”

  defgroup proab select=”segn PROA PROB”

Residue

or Res

All atoms in the residue expression enumerated.

  defgroup res41 select=”residue PROA 11”

  defgroup res41and51 select=”residue PROA 41 51”

  defgroup res41to60  select=”residue PROA 41:60”

atom

All atoms in the atom expression enumerated.

  defgroup c11 select=”atom PROA 11 C”

  defgroup cn11 select=”atom PROA 11 C N”

iatom

All atoms in the indexes list enumerated.  The index number starts from 0 to N-1 for N atoms system.

defgroup a0 select=”iatom  0”

defgroup a1_3 select=”iatom  1 3”

defgroup a10 select=”iatom  1:10”

range 1:10 means  1<= i <=10

iseq, or seq

All atoms in the residue sequence enumerated.

  defgroup res41and51 select=”seqn PROA && seq 41 51”

  defgroup res41to60  select=” seqn PROA && seq41:60”

mass

All atoms whose mass in the range given

  defgroup Call select=”mass  =8”

  defgroup heavyatom select=”mass  >2.1”

charge

All atoms whose partial charge in the range given

  Defgroup zeroch select=”charge  =0”

  Defgroup highch select=”charge >=0.5”

weight

All atoms whose weight in the range given

  Defgroup full  select=”weight >=1”

Rvdw

All atoms whose Van der Waals Radius in the range given

  defgroup smalla  select=”Rvdw  <=1.6”

Bfactor

All atoms whose temperatue factor in the range given

  defgroup hight select=”bfactor  >1.5”

X

Y

Z

All atoms whose coordinate in the range give

  Defgroup upa  select=”x  >=0  && y  >=0 && z  >=0”

toPoint

All atoms inside of radiation around a point

  defgroup sph10  select=”topoint 0 0 0 cutoff 10”

toLine

All atoms inside of radiation around a line

  defgroup tube10  select=”toline 0 0 0 0 0 1 cutoff 10”

Here,”0 0 0 0 0 1” define a line, the fisrt 3 real tell the point of line resident, and the last 3 real tell the direction of line

toPlane

All atoms inside of radiation around a plane

  defgroup block10 select=”toplane 0 0 1 0 cutoff 10”

Here, “0 0 1 0” is the plane control parameter a b c d respectively.

around

All atoms around of atoms specified

  defgroup protein select=”segn PROA”

defgroup around10 select=”around protein cutoff 10”

InRange

All atoms in the rectangular range specified

  defgroup box select=”inrange 0 0 0 20 20 20”

<expr>  &&  <expr>

And

<expr>  ||  <expr>

Or

!  <expr>

Not

Byres  <expr>

Extend selection to residues, i.e. if any one of atom in the residue is selected, all atoms in the residue will be selected.

Byseg  <expr>

Extend selection to segments, i.e. if any one of atom in the segment is selected, all atoms in the segment will be selected.