Jmol/Superposition: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis, Wayne Decatur

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 </nowiki>
 ==Demonstrations==
-<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
+<StructureSection load='' size='340' side='right' caption='superposition' scene='79/794960/Overall_both/1'>
-This is a default text for your page '''Karsten Theis/superpositions'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
-You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
+The opening scene is a result of the following script:
+ <nowiki>
+load files "=3HG5" "=3H54"
+restrict none  # display is cleared
+# define active site residues and superimpose structures
+define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A
+define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A
+compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~actnagal and *.CA}{~actgal and *.CA} ROTATE TRANSLATE
+select protein and 1.1; cartoon; color palegreen; center selected
+select 801-802; wireframe 100; color cpk
+select protein and 2.1; cartoon; color cornflowerblue;
+select 1000,2000; wireframe 100; color cpk
+select group within(3.0, (BMA, NAG, MAN)) and (sidechain or *.CA)
+select selected or (BMA, NAG, MAN); wireframe 50
+model 0
+</nowiki>
+It is nice to offer the viewer to look at the structures separately, or animate to go back and forth. This makes it easier to see the structures. The four buttons below were created with the following script:
+ <nowiki>
+<jmol>
+<jmolButton>
+<script>!exit; delay 1.2; model 1</script>
+  <text>GAL</text>
+</jmolButton>
+</jmol>
+<jmol>
+<jmolButton>
+<script>!exit; delay 1.5; model 2</script>
+  <text>NAGAL</text>
+</jmolButton>
+</jmol>
+<jmol>
+<jmolButton>
+<script>!exit; delay 1.5; model 0</script>
+  <text>both</text>
+</jmolButton>
+</jmol>
+<jmol>
+<jmolButton>
+<script>animation mode loop; animation on</script>
+  <text>animate</text>
+</jmolButton>
+</jmol></nowiki>
+<jmol>
+<jmolButton>
+<script>!exit; delay 1.2; model 1</script>
+  <text>GAL</text>
+</jmolButton>
+</jmol>
+<jmol>
+<jmolButton>
+<script>!exit; delay 1.5; model 2</script>
+  <text>NAGAL</text>
+</jmolButton>
+</jmol>
+<jmol>
+<jmolButton>
+<script>!exit; delay 1.5; model 0</script>
+  <text>both</text>
+</jmolButton>
+</jmol>
+<jmol>
+<jmolButton>
+<script>animation mode loop; animation on</script>
+  <text>animate</text>
+</jmolButton>
+</jmol>
 </StructureSection>