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Every atom in a PDB file has
a serial number - look at a PDB file using WordPad sometime and you'll
see exactly what I mean. These number also show up in some published
papers when a PDB file is being worked with.
select="atomno
= 131" a single
atom
select="atomno
217, atomno = 1426" two
atoms
select="atomno
>= 195 and atomno <= 277" a
range of atom serial numbers
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If you want to select all of
the atoms of a particular element in the molecule, you can do that, too... (Use
the full name, not the two-letter abbreviation)
select="magnesium"
Selects every Mg
atom in the molecule
select="
iron, sulfur" Selects
every Fe atom and every S atom in the molecule
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Atom PDB names...
PDB files name each atom in a standardized way (up to 4 characters). Alpha-carbons
are CA, beta-carbons CB, and so forth through CG, CD, CE, CZ, CH (gamma,
delta, epsilon, zeta, eta). Other examples are N7 (7th nitrogen in a residue),
O2P (second oxygen on a phosphorus), OE2 (second oxygen on an epsilon
carbon), HD1 (1st hydrogen on a delta carbon). To find out an atom's PDB
name, click on it. Its name is reported as the first word following "Atom:".
You can select, for example:
select="*.cg"
all carbons in gamma
position
select="lys.cg"
all lysine gamma-carbons
select=":a.cg"
all gamma-carbons in chain A
select="lys:a.cg"
all lysine gamma-carbons
in chain A
select="27-42:a.cg"
gamma-carbons in
chain A residues 27 through 42
select="*.h?"
all hydrogens with
2-character names
select="*.h???"
all hydrogens
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Chains...
Each polymer chain (polypeptide, nucleic acid, carbohydrate, etc.) has
a single character name (letter or digit). In a select command, this character
must be prefixed with a colon or an asterisk to signify that the letter
represents a chain. Most ATOM records in the PDB file are members of a
chain; sometimes all. Whether or not ligands of a chain are given the
same letter as the chain to which they bind, a different chain letter,
or no chain letter, varies. HETATM (hetero) atom records are considered
to be a "chain" only in the sense that they are all assigned the same
color by the "color chain" command. To find out what chain an atom belongs
to, click on it.
You could select:
select=":d"
all atoms in chain D
select="*d"
all atoms in chain D, again
select=":d,
:e" all
atoms in chains D or E
select="glu:2"
all glutamates
in chain 2
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