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Jaredsampson (talk | contribs) (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...) |
Jaredsampson (talk | contribs) (formatting for script) |
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| Line 3: | Line 3: | ||
Script to reproduce: | 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,\ | |
| − | + | -0.667115033, -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 | + | 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 |
Revision as of 04:07, 6 December 2018
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
File history
Click on a date/time to view the file as it appeared at that time.
| Date/Time | Thumbnail | Dimensions | User | Comment | |
|---|---|---|---|---|---|
| current | 03:25, 10 December 2018 |  | 800 × 800 (289 KB) | Cchem (talk | contribs) |
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