PDB File Naming
Conventions
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Index]
See Tutorial on Atom and Group Naming in PDF Files
(8) |
|
PDB Name
(case insensitive) |
Atom/Group
(only a partial listing) |
Examples:
command <expression> |
|
h n
ca
c o |
backbone H, N,
C-alpha, C, and O atoms joined in peptide bonds |
select (gly2.h,gly2.n,gly2.ca,gly2.c,gly2.o)
selects gly2 atoms joined in peptide bonds
select backbone and gly2 - an equivalent command |
|
ca
cb
cg
cd
ce
cg1 |
backbone alpha-C
sidechain beta-C
sidechain gamma-C
sidechain delta-C
sidechain epsilon-C branched sidechain C of val and ile |
select *.ca - selects all
a-Cs;
equals select alpha
select asp.cb - selects all
asp b-Cs
select glu141.cg
- selects g-C
of glu141
select gln77.cd - selects
d-C
of gln77
select lys30.cg
- selects e-C
of lys30
select *.cg1
- selects sidechain C's branched from b-C's
of all val and ile residues |
oe1,oe2
od1,od2
od2
oe1
oh |
sidechain glu O's
sidechain asp O's
sidechain asn O
sidechain gln O
sidechain tyr O |
select glu15.oe? - selects both
gamma-carboxylate sidechain O's of glu15
select (*.od1,od2) and asp99 - selects
both beta-carboxylate sidechain O's of asp99
select asn10.od2
- selects asn10 sidechain O
select *.oe1 - selects one sidechain O
of all glu and gln residues (Note: Both glu & gln have oe1 O
atoms.)
select tyr and *.oh - selects all
tyr sidechain O's |
nz
ne,nh1,nh2
nd1,ne2
nd2
ne2
ne1 |
sidechain lys epsilon-N
sidechain arg N's
sidechain his N's
sidechain asn N
sidechain gln N
sidechain trp N |
select lys101.nz - selects the sidechain
e-amino
N of lys101
select arg50.n?? and not backbone -
selects the 3 sidechain guanidinium N's of arg50
select sidechain and *.n?? and his149 -
selects 2 sidechain imidazole N's of his149
select *.nd2 - selects the sidechain N
of all asn residues (Note: Only asn has nd2 N atom.)
select *.ne2 - selects one sidechain N
of all gln and his residues (Note: Both gln & his have
ne2 atoms.)
select *.ne1 - selects sidechain N of
all trp residues (Note: Only trp has ne1 atom.) |
sd
sg |
sidechain met S
sidechain cys S |
select met44.sd - selects sidechain S of
met44
ssbonds on - connects (with a dotted line) sidechain S's of cys pairs
forming disulfide bonds |
asp###
etc. |
amino acid residue & no. |
select (asp1,glu)
- selects asp and all glu; equals
select acidic and 1 or glu |
|
protein |
all atoms making up protein |
restrict protein - restricts selected atoms
only to those making up protein |
|
hetero |
all non-protein, non-nucleic acid atoms |
define substrate hetero - defines a custom
group named "substrate" including all hetero atoms |
|
nucleic |
all atoms making up nucleic acids |
restrict nucleic - restricts selected atoms
to just those making up nucleic acids |
|
dna |
all atoms making up DNA |
select nucleic and not DNA - selects atoms
making up non-DNA nucleic acids, such as RNA |
