User:Wayne Decatur/SecStrFadeIn: Difference between revisions
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==Constructing animation== | ==Constructing animation== | ||
<Structure load='Insert PDB code or filename here' size='350' frame='true' align='right' caption='.' scene='60/607777/Surf_test/1' pspeed='8' /> | <Structure load='Insert PDB code or filename here' size='350' frame='true' align='right' caption='.' scene='60/607777/Surf_test/1' pspeed='8' /> | ||
<scene name='60/609822/1dtg_ball_stick_label/1'>1dtg ball and stick - STARTING SCENE</scene> | <scene name='60/609822/1dtg_ball_stick_label/1'>1dtg ball and stick - STARTING SCENE</scene> | ||
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</jmol> | </jmol> | ||
<jmol> | |||
<jmolLink> | |||
<script> load /wiki/scripts/60/609822/1dtg_ball_stick_label/1.spt; | |||
set echo top center;font echo 12 serif bolditalic;color echo white; echo "Start with all atoms of the protein|as small spheres connected by sticks..."; | |||
</script> | |||
<text>Making first part</text> | |||
</jmolLink> | |||
</jmol> | |||
<jmol> | |||
<jmolLink> | |||
<script> load /wiki/scripts/60/609822/1dtg_ball_stick_label/1.spt; | |||
set echo top center;font echo 12 serif bolditalic;color echo white; echo "Start with all atoms of the protein|as small spheres connected by sticks..."; | |||
delay 4.0; | |||
echo "Next hide all but the backbone atoms|keeping the connections shown..."; | |||
select protein and sidechain; | |||
var a = [1,2,3,4,5,6,7,8]; for(var i IN a) {color translucent @i; delay 0.4;}; | |||
delay 4.0; | |||
echo "The repeating patterns of the secondary structure|elements are starting to be noticeable."; | |||
</script> | |||
<text>Added 2nd part</text> | |||
</jmolLink> | |||
</jmol> | |||
<jmol> | |||
<jmolLink> | |||
<script> load /wiki/scripts/60/609822/1dtg_ball_stick_label/1.spt; | |||
set echo top center;font echo 12 serif bolditalic;color echo white; echo "Start with all atoms of the protein|as small spheres connected by sticks..."; | |||
delay 4.0; | |||
echo "Next hide all but the backbone atoms|keeping the connections shown..."; | |||
select protein and sidechain; | |||
var a = [1,2,3,4,5,6,7,8]; for(var i IN a) {color translucent @i; delay 0.4;}; | |||
delay 4.0; | |||
echo "The repeating patterns of the secondary structure|elements are starting to be noticeable."; | |||
delay 2.0; | |||
select protein; | |||
echo "To help with observing the patterns,|a tube tracing the backbone is revealed. "; | |||
var b = [0.01,0.05,0.1,0.2,0.3,0.4,0.45,0.5, 0.55]; for(var j IN b) {trace @j; delay 0.4;}; | |||
echo "And fade out the spheres and stick backbone.. "; | |||
var c = [0.55,0.5,0.4,0.2, 0.1,0.05,0.01]; for(var k IN c) {spacefill @k; wireframe @k; delay 0.4;}; | |||
wireframe off; speacefill off; | |||
</script> | |||
<text>Added 3rd part of progression from all atoms to cartoon</text> | |||
</jmolLink> | |||
</jmol> | |||
<jmol> | <jmol> | ||
<jmolLink> | <jmolLink> | ||
<script> load /wiki/scripts/60/609822/1dtg_ball_stick_label/1.spt; | <script> load /wiki/scripts/60/609822/1dtg_ball_stick_label/1.spt; | ||
set echo top center;font echo 12 serif bolditalic;color echo white; echo "Start with all atoms of the protein as small spheres connected by sticks..."; | set echo top center;font echo 12 serif bolditalic;color echo white; echo "Start with all atoms of the protein|as small spheres connected by sticks..."; | ||
delay 4.0; | |||
echo "Next hide all but the backbone atoms|keeping the connections shown..."; | |||
select protein and sidechain; | |||
var a = [1,2,3,4,5,6,7,8]; for(var i IN a) {color translucent @i; delay 0.4;}; | |||
delay 4.0; | |||
echo "The repeating patterns of the secondary structure|elements are starting to be noticeable."; | |||
delay 3.0; | |||
select protein; | |||
echo "To help with observing the patterns,|a tube tracing the backbone is revealed. "; | |||
var b = [0.01,0.05,0.1,0.2,0.3,0.4,0.45,0.5, 0.55]; for(var j IN b) {trace @j; delay 0.4;}; | |||
echo "And fade out the spheres and stick backbone.. "; | |||
var c = [0.55,0.5,0.4,0.2, 0.1,0.05,0.01]; for(var k IN c) {spacefill @k; wireframe @k; delay 0.4;}; | |||
wireframe off; spacefill off; | |||
echo "Finally fade in typical representation and|coloring of the secondary structure. "; | |||
color cartoon structure; | |||
var d = [0.55,0.5,0.4,0.2, 0.1,0.05,0.01]; for(var m IN d) { var n = 0.56 - m;cartoon @n; color cartoon translucent @n; trace @m; delay 0.4;}; | |||
trace off; delay 0.15; color cartoon translucent 0; cartoon on; | |||
</script> | </script> | ||
<text> | <text>Added 4th part of progression from all atoms to cartoon</text> | ||
</jmolLink> | </jmolLink> | ||
</jmol> | </jmol> | ||
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== Extras == | == Extras == | ||
{{Link Toggle FancyCartoonHighQualityView}} | {{Link Toggle FancyCartoonHighQualityView}} | ||
== References == | == References == | ||
<references/> | <references/> | ||
==See Also== | |||
* [[Proteopedia:Cookbook]] | |||
* [[Jmol/Interactivity]] | |||
Latest revision as of 22:36, 29 December 2020
Constructing animation
|
1dtg ball and stick - STARTING SCENE
Code in Page Versions To Use as Guides
(basic)
(with fancy cartoons)
Extras
References
