Talk:Garman lab: Interconversion of lysosomal enzyme specificities

Figure 1 panel B

load 3HG5
restrict none  # display is cleared
set ssbonds SIDECHAIN
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and (sidechain or *.CA) and *:A; wireframe 60; color bonds palegreen
select selected and not _C; spacefill 80; color cpk
set fontScaling ON
select (203,206) and *:A.CB; label %m%r; color label black;
select 801:A; wireframe 60; center selected
select (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA; trace 10; color cornflowerblue

load 3HG5
restrict none
select protein; cartoon; color palegreen; center selected
select 801-802; wireframe 100; color cpk
select group within(3.0, (BMA, NAG, MAN)) and sidechain
select selected or (BMA, NAG, MAN)
wireframe 50

Figure 1 panel C

load 3H54
restrict none  # display is cleared
set ssbonds SIDECHAIN
select (188,191,158,127,119,78,79,33,217,213,192,154,156) and (sidechain or *.CA) and *:A; wireframe 60; color bonds cornflowerblue
select selected and not _C; spacefill 80; color cpk
set fontScaling ON
select (188,191) and *:A.CB; label %m%r; color label black; font label 20
select a2g:A; wireframe 60; center selected
select (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA; trace 10; color cornflowerblue

load 3H54
restrict none
set hermiteLevel 6; set traceAlpha false
select protein; cartoon; color cornflowerblue; center selected
select a2g; wireframe 100; color cpk
select group within(3.0, (BMA, NAG, MAN)) and sidechain
select selected or (BMA, NAG, MAN)
wireframe 50

Figure 2 panel A

load 3lx9
restrict none  # display is cleared
set ssbonds SIDECHAIN
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and (sidechain or *.CA) and *:A; wireframe 60; color bonds yellow
select selected and not _C; spacefill 80; color cpk
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A.CB; label %m%r; color label black;
select a2g:A; wireframe 60; center selected
isosurface s_one color cornflowerblue "http://proteopedia.org/wiki/images/8/84/3lx9.jvxl" mesh

Figure 2 panel B

load 3lxa
restrict none  # display is cleared
set ssbonds SIDECHAIN
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and (sidechain or *.CA) and *:A; wireframe 60; color bonds yellow
select selected and not _C; spacefill 80; color cpk
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A.CB; label %m%r; color label black
select 801:A; wireframe 60; center selected

Figure 2 panel D

load 3lx9_3h54.pdb‎
restrict none  # display is cleared
set ssbonds SIDECHAIN
select (188,191,158,127,119,78,79,33,217,213,192,154,156) and (sidechain or *.CA) and *:A/2; wireframe 60; color bonds cornflowerblue
select selected and not _C; spacefill 80; color cpk
select (188,191) and *:A.CB/2; label %m%r; color label black; font label 20
select a2g:A/2; wireframe 60; center selected
select selected and _C; color skyblue
select (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA/2; trace 10; color cornflowerblue
select (47,92,93,134,142,168,170,172,203,206,207,227,231) and (sidechain or *.CA) and *:A/1; wireframe 60; color bonds yellow
select selected and not _C; spacefill 80; color cpk
select a2g:A/1; wireframe 60; center selected
select selected and _C; color gold