Talk:Garman lab: Interconversion of lysosomal enzyme specificities: Difference between revisions
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</nowiki> | </nowiki> | ||
Figure Y bonus | |||
<nowiki> | |||
load Image:Interconversion_model.pdb # do this in the scene authoring tool | |||
restrict none # display is cleared | |||
set ssBondsBackbone FALSE | |||
# show active site of alpha-GAL | |||
define ~actgal (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A/1 | |||
select ~actgal and (sidechain or *.CA); wireframe 60; color bonds palegreen | |||
select selected and not _C; spacefill 80; color cpk | |||
select (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA/1 | |||
trace 10; color palegreen | |||
select a2g:A; wireframe 60; | |||
select gla:A; wireframe 60; | |||
set fontScaling ON | |||
select (203,206) and *:A.CB/1; label %m%r; color label black; | |||
# show active site of alpha-NAGAL | |||
define ~actnagal (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A/2 | |||
select ~actnagal and (sidechain or *.CA); wireframe 60; color bonds cornflowerblue | |||
select selected and not _C; spacefill 80; color cpk | |||
select (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA/2; | |||
trace 10; color cornflowerblue | |||
select 801:A; wireframe 60; center selected | |||
select a2g:A; wireframe 60; | |||
select (188,191) and *:A.CB/2; label %m%r; color label black; font label 14 | |||
# one of the lines below for the four different figures | |||
contact {a2g:A/1}{~actgal} full | |||
contact {gla:A/1}{~actgal} full | |||
contact {gla:A/2{~actnagal} full | |||
contact {a2g:A/2}{~actnagal} full | |||
# hide one of the sugars (depending which contacts we are showing | |||
hide a2g | |||
hide gla | |||
</nowiki> | |||
Figure 2 panel A | Figure 2 panel A | ||
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select 1.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA; | select 1.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA; | ||
trace 10; color cornflowerblue | trace 10; color cornflowerblue | ||
select 1000:A; wireframe 60; | select 1.1 and 1000:A; wireframe 60; | ||
select | select selected and _C; color skyblue; | ||
select 2.1 and ~act2 and (sidechain or *.CA); wireframe 60; color bonds yellow | select 2.1 and ~act2 and (sidechain or *.CA); wireframe 60; color bonds yellow | ||
select selected and not _C; spacefill 80; color cpk | select selected and not _C; spacefill 80; color cpk | ||
select 2.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA; | select 2.1 and (46-48, 91-94, 133-135, 141-143, 169-173, 202-208, 226-232) and *:A.CA; | ||
trace 10; color yellow | trace 10; color yellow | ||
select 1000:A; wireframe 60; | select 2.1 and 1000:A; wireframe 60; | ||
select selected and _C; color beige; center selected | |||
</nowiki> | </nowiki> | ||