User:Karsten Theis/AI tutorial: Difference between revisions
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Typically, the foreground is shown at the detail of single atoms (represented by wireframe, spacefill, both "ball-and-stick", surfaces), and it is the center of rotation. Often, the background is shown with thinner lines, uniform color, or not showing single atoms but groups (represented by backbone, cartoon, meshribbon, ribbon, strand, trace, or surface). If the viewer is encouraged to rotate 360 degrees, the background should not interfere with seeing the foreground (use thin lines, slabbing, fading/fogging "zshade"). Transparency should be used with caution in Jmol because it can add visual clutter (spacefill and thick wireframe as well as cartoons add clutter, strands of constant thickness work well). | Typically, the foreground is shown at the detail of single atoms (represented by wireframe, spacefill, both "ball-and-stick", surfaces), and it is the center of rotation. Often, the background is shown with thinner lines, uniform color, or not showing single atoms but groups (represented by backbone, cartoon, meshribbon, ribbon, strand, trace, or surface). If the viewer is encouraged to rotate 360 degrees, the background should not interfere with seeing the foreground (use thin lines, slabbing, fading/fogging "zshade"). Transparency should be used with caution in Jmol because it can add visual clutter (spacefill and thick wireframe as well as cartoons add clutter, strands of constant thickness work well). | ||
The initial scene: Chymotrypsin active site | |||
<nowiki> | |||
load =7GCH # Chymotrypsin with covalently bound inhibitor | |||
restrict none # clean slate | |||
define ~focal 57, 102, 195, LPF # foreground: catalytic triad and inhibitor | |||
select LPF.C2 or 195.CB; bondOrder single; # ensure covalent bond | |||
select ~focal; Spacefill 25%; wireframe 0.36 # ball-and-stick for foreground | |||
center selected; zoom 300; # | |||
select LPF.CP1, LPF.CP2, LPF.CP3, LPF.CP4, LPF.CP5, LPF.CP6; # aromatic ring of inhibitor | |||
color atoms opaque [xda70d6]; # magenta | |||
select LPF and not selected; color atoms opaque [xe6e6fa]; # rest of inhibitor: lavender??? | |||
select not ~focal; color chain; # default chain colors (aquarell) | |||
select protein and not ~focal; Spacefill 100%; # background as spacefill | |||
select 57.CD2, 102.OD1, 195.CB; label "%n %r"; # labelled atoms | |||
color label [x000000]; font label 13 SansSerif Bold; # white labels, chose font | |||
select 57.CD2; set labelOffset -4 4; # each label has a different offset | |||
select 102.OD1; set labelOffset 1 1; # | |||
select 195.CB; set labelOffset 0 -1; # | |||
background black; set zshade on # the background is almost not visible affects zshade | |||
moveto 0.0 { -97 855 -510 89.56} 300.0 0.0 0.0 {38.343720000000005 74.45217999999998 85.45410000000003} 34.78371098010064 {0 0 0} 0 0 0 3.0 0.0 0.0; | |||
</nowiki> | |||
<nowiki> | <nowiki> | ||
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center selected; zoom 300 # center and zoom in | center selected; zoom 300 # center and zoom in | ||
</nowiki> | </nowiki> | ||
===Overall views=== | ===Overall views=== | ||
These don't have a focal point. They should be centered on everything displayed. If using a representation you can look through (e.g. backbone or cartoon rather than surface or spacefill), fading/fogging "zshade" may be helpful to distinguish front and back. | These don't have a focal point. They should be centered on everything displayed. If using a representation you can look through (e.g. backbone or cartoon rather than surface or spacefill), fading/fogging "zshade" may be helpful to distinguish front and back. | ||
