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PyMOL>unset pdb_hetatm_guess_valences
Setting: pdb_hetatm_guess_valences set to off.
PyMOL>reinitialize store_defaults
PyMOL>load dat/odd01.pdb
CmdLoad: "dat/odd01.pdb" loaded as "odd01".
PyMOL>iterate all, print name
CZ
NH1
NH2
HE
HH11
HH12
HH21
HH22
CA
CA
OA22
OA23
ABCD
LMN
XYZ
PE
O1B
AC5
Iterate: iterated over 18 atoms.
PyMOL>save cmp/C0700odd.1.pdb
Save: wrote "cmp/C0700odd.1.pdb".
PyMOL>set retain_order
Setting: retain_order set to 1.
PyMOL>iterate all, print name
HE
CZ
NH1
HH11
HH12
NH2
HH21
HH22
CA
CA
OA22
OA23
ABCD
XYZ
LMN
PE
O1B
AC5
Iterate: iterated over 18 atoms.
PyMOL>save cmp/C0700odd.2.pdb
Save: wrote "cmp/C0700odd.2.pdb".
PyMOL>set pdb_no_end_record
Setting: pdb_no_end_record set to on.
PyMOL>save cmp/C0700odd.3.pdb
Save: wrote "cmp/C0700odd.3.pdb".
PyMOL>set pdb_retain_ids
Setting: pdb_retain_ids set to on.
PyMOL>save cmp/C0700odd.4.pdb
Save: wrote "cmp/C0700odd.4.pdb".
PyMOL>reinit
PyMOL>set retain_order
Setting: retain_order set to 1.
PyMOL>load dat/odd01.pdb
CmdLoad: "dat/odd01.pdb" loaded as "odd01".
PyMOL>iterate all,print name
HE
CZ
NH1
HH11
HH12
NH2
HH21
HH22
CA
CA
OA22
OA23
ABCD
XYZ
LMN
PE
O1B
AC5
Iterate: iterated over 18 atoms.
PyMOL>set pdb_reformat_names_mode, 1
Setting: pdb_reformat_names_mode set to 1.
PyMOL>save cmp/C0700odd.5.pdb
Save: wrote "cmp/C0700odd.5.pdb".
PyMOL>dele all
PyMOL>load cmp/C0700odd.3.pdb
CmdLoad: "cmp/C0700odd.3.pdb" loaded as "C0700odd.3".
PyMOL>set pdb_reformat_names_mode, 0
Setting: pdb_reformat_names_mode set to 0.
PyMOL>save cmp/C0700odd.6.pdb
Save: wrote "cmp/C0700odd.6.pdb".
PyMOL>iterate all,print name
HE
CZ
NH1
1HH1
2HH1
NH2
1HH2
2HH2
CA
CA
2OA2
3OA2
ABCD
XYZ
LMN
PE
O1B
AC5
Iterate: iterated over 18 atoms.
PyMOL>reinit
PyMOL>set pdb_reformat_names_mode, 1
Setting: pdb_reformat_names_mode set to 1.
PyMOL>load cmp/C0700odd.3.pdb
CmdLoad: "cmp/C0700odd.3.pdb" loaded as "C0700odd.3".
PyMOL>iterate all,print name
CZ
NH1
NH2
HE
1HH1
2HH1
1HH2
2HH2
CA
CA
2OA2
3OA2
ABCD
LMN
XYZ
PE
O1B
AC5
Iterate: iterated over 18 atoms.
PyMOL>save cmp/C0700odd.7.pdb
Save: wrote "cmp/C0700odd.7.pdb".
PyMOL>set pdb_reformat_names_mode,2
Setting: pdb_reformat_names_mode set to 2.
PyMOL>save cmp/C0700odd.8.pdb
Save: wrote "cmp/C0700odd.8.pdb".
PyMOL>dele all
PyMOL>load cmp/C0700odd.5.pdb
CmdLoad: "cmp/C0700odd.5.pdb" loaded as "C0700odd.5".
PyMOL>iterate all,print name
CZ
NH1
NH2
HE
HH11
HH12
HH21
HH22
CA
CA
OA22
OA23
ABCD
LMN
XYZ
PE
O1B
AC5
Iterate: iterated over 18 atoms.
PyMOL>set pdb_reformat_names_mode,0
Setting: pdb_reformat_names_mode set to 0.
PyMOL>save cmp/C0700odd.9.pdb
Save: wrote "cmp/C0700odd.9.pdb".
PyMOL>set pdb_reformat_names_mode,1
Setting: pdb_reformat_names_mode set to 1.
PyMOL>save cmp/C0700odd.A.pdb
Save: wrote "cmp/C0700odd.A.pdb".
PyMOL>set pdb_literal_names, 1
Setting: pdb_literal_names set to on.
PyMOL>save cmp/C0700odd.B.pdb
Save: wrote "cmp/C0700odd.B.pdb".
PyMOL>dele all
PyMOL>load cmp/C0700odd.3.pdb
CmdLoad: "cmp/C0700odd.3.pdb" loaded as "C0700odd.3".
PyMOL>iterate all,print name
CZ
HE
NH1
NH2
HH11
HH12
HH21
HH22
CA
CA
OA22
OA23
LMN
XYZ
ABCD
O1B
PE
AC5
Iterate: iterated over 18 atoms.
PyMOL>dele all
PyMOL>load cmp/C0700odd.5.pdb
CmdLoad: "cmp/C0700odd.5.pdb" loaded as "C0700odd.5".
PyMOL>iterate all,print name
CZ
HE
NH1
NH2
1HH1
2HH1
1HH2
2HH2
CA
CA
2OA2
3OA2
LMN
XYZ
ABCD
O1B
PE
AC5
Iterate: iterated over 18 atoms.
PyMOL>reinit
PyMOL>load dat/small02.pdb
CmdLoad: "dat/small02.pdb" loaded as "small02".
PyMOL>save cmp/C0700odd.C.pdb
Save: wrote "cmp/C0700odd.C.pdb".
PyMOL>reinit
PyMOL>set pdb_reformat_names_mode, 1
Setting: pdb_reformat_names_mode set to 1.
PyMOL>load dat/small02.pdb
CmdLoad: "dat/small02.pdb" loaded as "small02".
PyMOL>iterate all, print name
CL16
C1
C4
C6
C9
N12
C13
C17
C19
C20
C22
C25
C28
C29
C30
N32
C33
C35
C39
C40
C41
C42
C43
C46
C49
C51
N54
C55
N56
O57
C58
C61
O64
C65
BR37
BR38
Iterate: iterated over 36 atoms.
PyMOL>save cmp/C0700odd.D.pdb
Save: wrote "cmp/C0700odd.D.pdb".
PyMOL>set pdb_reformat_names_mode, 2
Setting: pdb_reformat_names_mode set to 2.
PyMOL>load dat/small02.pdb
CmdLoad: "dat/small02.pdb" appended into object "small02", state 2.
PyMOL>iterate all, print name
CL16
C1
C4
C6
C9
N12
C13
C17
C19
C20
C22
C25
C28
C29
C30
N32
C33
C35
C39
C40
C41
C42
C43
C46
C49
C51
N54
C55
N56
O57
C58
C61
O64
C65
BR37
BR38
Iterate: iterated over 36 atoms.
PyMOL>save cmp/C0700odd.E.pdb
Save: wrote "cmp/C0700odd.E.pdb".
PyMOL>reinit
PyMOL>set pdb_literal_names
Setting: pdb_literal_names set to on.
PyMOL>set retain_order
Setting: retain_order set to 1.
PyMOL>set pdb_retain_ids
Setting: pdb_retain_ids set to on.
PyMOL>set pdb_no_end_record
Setting: pdb_no_end_record set to on.
PyMOL>unset pdb_use_ter_records
Setting: pdb_use_ter_records set to 0.
PyMOL>load dat/odd01.pdb
CmdLoad: "dat/odd01.pdb" loaded as "odd01".
PyMOL>save cmp/C0700odd.F.pdb
Save: wrote "cmp/C0700odd.F.pdb".
PyMOL>reinit
PyMOL>load dat/helix_amber.pdb
CmdLoad: "dat/helix_amber.pdb" loaded as "helix_amber".
PyMOL>iterate resi 2, print name, elem
N N
CA C
C C
O O
CB C
SG S
H H
HA H
HB2 H
HB3 H
N N
CA C
C C
O O
CB C
H H
HA H
HB1 H
HB2 H
HB3 H
Iterate: iterated over 20 atoms.
PyMOL>reinit
PyMOL>load dat/odd02.pdb
CmdLoad: "dat/odd02.pdb" loaded as "odd02".
PyMOL>iterate all, print name, elem
C C
O O
CG C
CD C
NE N
CZ C
NH1 N
NH2 N
HG1 H
HG2 H
HD1 H
HD2 H
HE H
HH11 H
HH12 H
HH21 H
Hh22 Hh
N N
CA C
C C
O O
CB C
CG1 C
CG2 C
HN H
HA H
HB H
HG11 H
HG12 H
HG21 H
HG22 H
HG23 H
Hg13 Hg
N N
CA C
HN H
Iterate: iterated over 36 atoms.
PyMOL>save cmp/C0700.odd.G.pdb
Save: wrote "cmp/C0700.odd.G.pdb".
PyMOL>set pdb_reformat_names_mode,1
Setting: pdb_reformat_names_mode set to 1.
PyMOL>save cmp/C0700.odd.H.pdb
Save: wrote "cmp/C0700.odd.H.pdb".
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