3D_biomolecule 0x2 *, PDB:1a34
3D_color #ff0000
3D_highlight_selected_amino_acids 2000
3D_highlight_selected_atoms 2000
3D_label_color #ff0000
3D_native jmol, 3D_label "This label appears only under Jmol"
3D_native astex, 3D_label "This label appears only under Astex"
3D_select 69.CA
3D_select NADH
3D_zoom 200%
DAS_features CSA%20-%20extended uniprot cbs_total netphos netoglyc , UNIPROT:P29590
GFF P25787 UniProtKB Modified residue 24 24 . . . Note=Phosphotyrosine
GFF http://server/path/myGffFile.gff
aa_sequence -VLSAAERAQVKAAWGKI--QAGAHGAEALERMFLGFPTTKTYPF, Xenopus
accession_id UNIPROT:HSLV_ECOLI , hslv_ecoli
add_annotation Balloon=My text, myProtein.pdb/myAnnotation1,
add_annotation Balloon="<HTML><BODY>My text with <b>bold</b> or <u>underline</u></BODY></HTML>", myProtein.pdb/myAnnotation1,
add_compound PDB:1gd2_A PDB:1gd2_B, 1gd2_E.pdb
add_xref PDB:1NED, hslv_ecoli
align *
sequence1/20-30 sequence2/22-40
balloon_text bla bla , sequence1
bg_color 20-30=#00FF00, sequence1
bg_color 20:-30:=#00FF00, sequence2
clip_N_term sequence1/100
clip_N_term sequence1/nameOfResidueSelection
clip_N_term sequence1
echo Hello world
feature_colors Modified_residue=#FF2222,#FF0000 Phosphorylated_residue=#AAaa00 Glycosylated_residue=#00ffFF
icon http://www.bioinformatics.org/strap/images/dog.png , protein
icon NULL , protein
icon data:image/gif;base64,R0lGODlhGgAaAIABADMzM////yH5BAEKAAEALAAAAAAaABoAAAI5jI+py+0Po0SgWmpry9nwq3yimIwmh51nqo5s+71wd8yuPIc2Xe7AZnvkIK3JauJBIVlLXfMJjUIKADs= , 4 5
let $x=protein/selection
new_selection 20-30, $x
color #00ff00, $x
new_selection 1-20, my_protein/N-terminus
new_selection 10:-20: 30:, my_protein/a_selection
project_coordinates PDB:1BOR_A , UNIPROT:P29590
project_coordinates AUTO , UNIPROT:P29590
project_coordinates NULL , UNIPROT:P29590
put_property NOT_USE_STRUCTURE_FOR_ALIGNMENT=true , *
put_property NOT_USE_STRUCTURE_FOR_ALIGNMENT=NULL , *
-0.51 -0.69 0.50 0.22 0.45 0.86 -0.82 0.55 -0.80 91.15 25.13 55.68 , protein
NULL, protein
secondary_structure ---HHHHHH---HHHHH---EEEEEEEEEE----EEEEEE , Xenopus
select_3D ViewID
select_3D ViewID , subtilisin
select_3D ViewID , subtilisin/100-200
set_characters_per_line 60
color #00FF00 , sequence1
color #00FF0066 , sequence1
set_color_mode hydropathy
set_conservation_threshold 70
Eukaryota;Metazoa;Craniata;Vertebrata;Euteleostomi;Mammalia;Primates;Hominidae;Homo, sequences1
taxonomy_group Primates, *
superimpose *
taxonomy_group Vertebrata Viruses Eukaryota Bacteria Archaea Fungi Mammalia, *
cds join(10 20..30) , protein
cds complement(join(10 20..30)) , myProtein
cds 1.. , myProtein
cds 2 , myProtein
tree *
find_uniprot_id *
uniprot_features *
alias_for_url WIKTIONARY:=http://en.wiktionary.org/wiki/
balloon WIKTIONARY:happy , sequence
bg align *
... some script lines ...
wait_for align