User:Karsten Theis/AI tutorial: Difference between revisions

load files "=3H54" "=3LX9"                                                           # load 2 files, they are selected as 1.1 and 2.1 below

restrict none                                                                         # display is cleared

define ~act2 2.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A       # active site residues of 3LX9

define ~act1 1.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A       # active site residues of 3H54

compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~act2}{~act1} ROTATE TRANSLATE                 # superposition (different sequences, so use alpha carbon)

set ssbonds SIDECHAIN                                                                 # disulfide bonds are anchored on SG, not on CA

select 1.1 and ~act1 and (sidechain or *.CA); wireframe 60;                           # show the active site as wireframe

color bonds cornflowerblue                                                           # 3H54 is shown in blue (just the bonds)

select selected and not _C; spacefill 80; color cpk                                   # spacefill, atoms other than carbon shown using CPK color scheme

select 1.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA;# some main chain context for the active site residues  

select 1.1 and 1000:A; wireframe 60;                                                 # selecting the sugar in 3H54

select selected and _C; color skyblue;                                               # carbons in skyblue

select 2.1 and ~act2 and (sidechain or *.CA); wireframe 60;                           # show the active site as wireframe  

color bonds yellow                                                                   # 3LX9 is shown in yellow (just the bonds)

select selected and not _C; spacefill 80; color cpk                                   # spacefill, atoms other than carbon shown using CPK color scheme

select 2.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA;# some main chain context for the active site residues

select 2.1 and 1000:A; wireframe 60;;                                                 # selecting the sugar in 3LX9  

select selected and _C; color beige;                                                 # carbons in beige

center selected; zoom 300                                                             # center and zoom in