Difference between revisions of "File:4gms colors.png"

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(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...)
 
(formatting for script)
 
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,\
+
    -0.718157351,    0.514449000,  -0.468602538,\
    -0.667115033,  -0.317360103,    0.673974276,\
+
    -0.667115033,  -0.317360103,    0.673974276,\
    0.198008969,    0.796632588,    0.571111977,\
+
      0.198008969,    0.796632588,    0.571111977,\
    0.000045628,  -0.000060942,  -75.169761658,\
+
      0.000045628,  -0.000060942,  -75.169761658,\
    20.388980865,  -23.567779541,  38.543788910,\
+
    20.388980865,  -23.567779541,  38.543788910,\
    52.026283264,  98.326217651,  -20.000000000 )
+
    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

Latest revision as of 00:07, 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/TimeThumbnailDimensionsUserComment
current00:04, 6 December 2018Thumbnail for version as of 00:04, 6 December 2018800 × 800 (289 KB)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...
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