File:4gms colors.png - Revision history

Cchem: Cchem uploaded "File:4gms colors.png"

2018-12-10T03:25:56Z

Cchem uploaded "File:4gms colors.png"

Cchem: 2 revisions

2018-12-10T03:24:45Z

2 revisions

Jaredsampson: formatting for script

2018-12-06T04:07:14Z

formatting for script

Jaredsampson: Prepared in response to a pymol-users thread from 11/30/2018-12/5/2018 about the appearance of transparency in a published figure. Script to reproduce: bg_color white fetch 4gms, async=0 # hemagglutinin selections select ha, chain A select l130, ha...

2018-12-06T04:04:52Z

New page

Prepared in response to a pymol-users thread from 11/30/2018-12/5/2018 about the appearance of transparency in a published figure.

Script to reproduce:

bg_color white
fetch 4gms, async=0

# hemagglutinin selections
select ha, chain A
select l130, ha and resi 133-138
select l150, ha and resi 155-163
select h190, ha and resi 187-196
select l220, ha and resi 225-228
select loops, l130 or l150 or h190 or l220

# antibody selection
select h2, chain H and resi 51-59
deselect

# basic view
hide everything
as cartoon, ha
as cartoon, h2
cartoon tube

# colors
color orange, h2
color palecyan, ha
color deepteal, loops

set_view (\
-0.718157351, 0.514449000, -0.468602538,\
-0.667115033, -0.317360103, 0.673974276,\
0.198008969, 0.796632588, 0.571111977,\
0.000045628, -0.000060942, -75.169761658,\
20.388980865, -23.567779541, 38.543788910,\
52.026283264, 98.326217651, -20.000000000 )

set ray_opaque_background, 1
png 4gms_colors.png, height=800, width=800, ray=1

← Older revision	Revision as of 03:25, 10 December 2018
(No difference)

← Older revision	Revision as of 03:24, 10 December 2018
(No difference)

@@ Line 3: / Line 3: @@
 Script to reproduce:
-bg_color white
+ bg_color white
-fetch 4gms, async=0
+ fetch 4gms, async=0
-−
-# hemagglutinin selections
+ # hemagglutinin selections
-select ha, chain A
+ select ha, chain A
-select l130, ha and resi 133-138
+ select l130, ha and resi 133-138
-select l150, ha and resi 155-163
+ select l150, ha and resi 155-163
-select h190, ha and resi 187-196
+ select h190, ha and resi 187-196
-select l220, ha and resi 225-228
+ select l220, ha and resi 225-228
-select loops, l130 or l150 or h190 or l220
+ select loops, l130 or l150 or h190 or l220
-−
-# antibody selection
+ # antibody selection
-select h2, chain H and resi 51-59
+ select h2, chain H and resi 51-59
-deselect
+ deselect
-−
-# basic view
+ # basic view
-hide everything
+ hide everything
-as cartoon, ha
+ as cartoon, ha
-as cartoon, h2
+ as cartoon, h2
-cartoon tube
+ cartoon tube
-−
-# colors
+ # colors
-color orange, h2
+ color orange, h2
-color palecyan, ha
+ color palecyan, ha
-color deepteal, loops
+ color deepteal, loops
-−
-set_view (\
+ set_view (\
-    -0.718157351,    0.514449000,   -0.468602538,\
+     -0.718157351,    0.514449000,   -0.468602538,\
-    -0.667115033,   -0.317360103,    0.673974276,\
+     -0.667115033,   -0.317360103,    0.673974276,\
 .198008969,    0.796632588,    0.571111977,\
 .000045628,   -0.000060942,  -75.169761658,\
 .388980865,  -23.567779541,   38.543788910,\
 .026283264,   98.326217651,  -20.000000000 )
-−
-set ray_opaque_background, 1
+ set ray_opaque_background, 1
-png 4gms_colors.png, height=800, width=800, ray=1
+ png 4gms_colors.png, height=800, width=800, ray=1