#STRAP_SCRIPT Also see http://www.bioinformatics.org/strap/web/strap_script.html # Lines starting with a hash sign are not evaluated. # Commands like 3D_sticks that start with "3D_" are evaluated by # the 3D-view previously selected by "select_3D". # All other commands are evaluated by Strap. # Certain time consuming jobs are run in the background when preceeded by a "bg". # For waiting for the to finish use "wait_for". # For the specification of protein names and selection names, # regular expressions can be used # Previously loaded proteins will be hidden, not deleted. hide * # The load command takes URLs or database IDs, # optionally followed by vertical bar and a protein name. load UNIPROT:PSA4_drome|a3_DrosophilaMelanogaster UNIPROT:PSA4_human|a3_HomoSapiens UNIPROT:PSA2_XENLA|a2_XenopusLaevis # Alignment as a background process. bg align * load PDB:1ned_A|hs_EscherichiaColi load PDB:1ryp_V|b1_SaccharomycesCerevisiae PDB:1ryp_O|a1_SaccharomycesCerevisiae wait_for align bg align * # If 3D-view View_a1b1hs exists, then close it. close_3D View_a1b1hs # Next we create a 3D view with 3 proteins. # This view's name will be "View_a1b1hs". open_3D View_a1b1hs, hs_EscherichiaColi a1_SaccharomycesCerevisiae b1_SaccharomycesCerevisiae # Wait 2 seconds sleep 2000 wait_for align superimpose * # 3D-view commands for a1_SaccharomycesCerevisiae select_3D View_a1b1hs, a1_SaccharomycesCerevisiae 3D_select $ALL 3D_cartoon off 3D_lines off 3D_color #FF0000 3D_ribbons on # 3D-view commands for a1_SaccharomycesCerevisiae select_3D View_a1b1hs, b1_SaccharomycesCerevisiae 3D_select $ALL 3D_cartoon off 3D_lines off 3D_color #0000FF # Next we select only the main chain atoms. 3D_select 1-196.C.CA.CB.N.O 3D_lines on 3D_select $ALL 3D_ribbons on 3D_select 33,129 3D_color #0000FF 3D_sticks on 3D_select 1.CA 3D_spheres on 3D_select 33.CA 3D_label "Atom CA of Lys 33" 3D_select "MG" 3D_color #FF00FF 3D_spheres on 3D_label "This is Magnesium" # 3D-view commands for hs_EscherichiaColi select_3D View_a1b1hs, hs_EscherichiaColi 3D_select $ALL 3D_cartoon off 3D_lines off 3D_color #00FF00 3D_ribbons on 3D_select 1 3D_center # We create some named residue selection. # They will be underlined in the sequence new_selection 1: , b1_SaccharomycesCerevisiae/catalytic new_selection 1: , hs_EscherichiaColi/catalytic set_annotation Color=#FFFF00, hs_EscherichiaColi/catalytic b1_SaccharomycesCerevisiae/catalytic add_annotation Balloon=The N-Termini Threonine is important for catalysis. In 1ryp, it is exchanged by an alanine, hs_EscherichiaColi/catalytic b1_SaccharomycesCerevisiae/catalytic new_selection 1-20 , a1_SaccharomycesCerevisiae/N-terminus add_annotation Balloon=The N-Termini of alpha subunits form a meshwork to control, what proteins get into the barrel. , a1_SaccharomycesCerevisiae/N-terminus, add_annotation Balloon=Double click to see publication refs, a1_SaccharomycesCerevisiae/N-terminus add_annotation Note=PMID18471981 PMID20360109 , a1_SaccharomycesCerevisiae/N-terminus new_selection 1-9, b1_SaccharomycesCerevisiae/N-terminus add_annotation Balloon=The N-Terminus is cleaved off in an autocatalytical process. In the mature subunit there is an n-terminal Serine-1, b1_SaccharomycesCerevisiae/N-terminus # DAS seems not to be supported any more # DAS_features CSA%20-%20extended uniprot cbs_total netphos netoglyc , * # Instead using uniprot_features uniprot_features * # Icons could be set by URL but we will do it with base64 # icon http://www.nih.gov/science/models/Schizosaccharomyces/images/pombelarge.jpg, .*charomyces.* # icon http://bioweb.uwlax.edu/bio203/s2008/moder_just/Images/800px-E_coli_at_10000x.jpg, .*Escherichia.* # icon http://www.goldenweb.it/software/immagini/icone/animals/water_animals/Frog.gif, .*Xenopus.* # icon http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/templates/gif/species/transparent/hum_temp.gif, .*HomoSapiens.* # icon http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/templates/gif/species/transparent/fly_temp.gif, .*Drosophila.* # Refering to proteins, regular expressions are allowed like in the following: icon image/png;base64,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, .*Xenopus.* icon image/png;base64,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, .*HomoSapiens.* icon image/png;base64,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, .*Drosophila.* select_3D View_a1b1hs, a1_SaccharomycesCerevisiae 3D_select 11-20 # Next we give a hex color with transparency 0x77: 3D_surface_color #77FF00FF 3D_surface on 3D_select 69.CA 3D_label "This is the label text"