User:Angel Herraez/Sandbox 3

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(New page: == Testing accented characters in green links ==)
Current revision (19:43, 13 December 2016) (edit) (undo)
(Undo revision 2697136 by Angel Herraez (Talk))
 
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== Testing accented characters in green links ==
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== Alternate rendering for display of both evolutionary conservation and allosteric site ==
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This is a proof-of-concept.
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<StructureSection load='1b86' size='340' side='right' caption='Hemoglobin' scene=''>
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=== Hemoglobin with 2,3-BPG and oxygen ===
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As a reference: <scene name='38/388991/Default_rendering/3'>default Proteopedia rendering</scene>
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1) You must first apply <scene name='38/388991/Evolcons_rendering/1'>Proteopedia rendering for Evol.Cons.</scene>
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2) Then <jmol>
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<jmolButton>
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<text>get prepared</text>
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<script>
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/* define sites */
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define ~allosteric [HOH]43:B,[HOH]68:B,[HOH]121:B,[HOH]122:B,[HOH]124:B,[VAL]144:B,[HIS]145:B.N,[HIS]145:B.CA,[HIS]145:B.C,[HIS]145:B.O,[HIS]145:B.CB,[HIS]145:B.CG,[HIS]145:B.CD2,[HIS]145:B.ND1,[HIS]145:B.CE1,[HIS]145:B.NE2,[LYS]225:B.N,[LYS]225:B.CA,[LYS]225:B.C,[LYS]225:B.O,[LYS]225:B.CB,[LYS]225:B.CG,[LYS]225:B.CD,[LYS]225:B.CE,[LYS]225:B.NZ,[GLY]279:B.N,[GLY]279:B.CA,[GLY]279:B.C,[GLY]279:B.O,[ASN]282:B.N,[ASN]282:B.CA,[ASN]282:B.C,[ASN]282:B.O,[ASN]282:B.CB,[ASN]282:B.CG,[ASN]282:B.ND2,[ASN]282:B.OD1,[ALA]283:B.N,[ALA]283:B.CA,[ALA]283:B.C,[ALA]283:B.O,[ALA]283:B.CB,[HIS]286:B.N,[HIS]286:B.CA,[HIS]286:B.C,[HIS]286:B.O,[HIS]286:B.CB,[HIS]286:B.CG,[HIS]286:B.CD2,[HIS]286:B.ND1,[HIS]286:B.CE1,[HIS]286:B.NE2,[HOH]21:D.O,[HOH]83:D.O,[HOH]102:D.O,[HOH]103:D.O,[HOH]104:D.O,[HOH]105:D.O,[HOH]106:D.O,[HOH]107:D.O,[HOH]108:D.O,[HOH]109:D.O,[HOH]110:D.O,[HOH]111:D.O,[HOH]112:D.O,[HOH]113:D.O,[HOH]114:D.O,[HOH]115:D.O,[HOH]117:D.O,[HOH]118:D.O,[HOH]119:D.O,[HOH]123:D.O,[VAL]544:D.N,[VAL]544:D.CA,[VAL]544:D.C,[VAL]544:D.O,[VAL]544:D.CB,[VAL]544:D.CG1,[VAL]544:D.CG2,[HIS]545:D.N,[HIS]545:D.CA,[HIS]545:D.C,[HIS]545:D.O,[HIS]545:D.CB,[HIS]545:D.CG,[HIS]545:D.CD2,[HIS]545:D.ND1,[HIS]545:D.CE1,[HIS]545:D.NE2,[LYS]625:D.N,[LYS]625:D.CA,[LYS]625:D.C,[LYS]625:D.O,[LYS]625:D.CB,[LYS]625:D.CG%A,[LYS]625:D.CG%B,[LYS]625:D.CD%A,[LYS]625:D.CD%B,[LYS]625:D.CE%A,[LYS]625:D.CE%B,[LYS]625:D.NZ%A,[LYS]625:D.NZ%B,[ASN]682:D.N,[ASN]682:D.CA,[ASN]682:D.C,[ASN]682:D.O,[ASN]682:D.CB,[ASN]682:D.CG,[ASN]682:D.ND2,[ASN]682:D.OD1,[HIS]686:D.N,[HIS]686:D.CA,[HIS]686:D.C,[HIS]686:D.O,[HIS]686:D.CB,[HIS]686:D.CG,[HIS]686:D.CD2,[HIS]686:D.ND1,[HIS]686:D.CE1,[HIS]686:D.NE2,[DG2]701:D.P1,[DG2]701:D.P6,[DG2]701:D.O2,[DG2]701:D.C3,[DG2]701:D.C4,[DG2]701:D.O5,[DG2]701:D.C7,[DG2]701:D.O7,[DG2]701:D.O8,[DG2]701:D.O9,[DG2]701:D.O10,[DG2]701:D.O11,[DG2]701:D.O13,[DG2]701:D.O14,[DG2]701:D.O15;
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define ~ligand [DG2]701:D;
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/* common script */
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define temp selected;
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select protein; trace -1.0; color trace chain;
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select ~allosteric; cpk on;
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select ~allosteric and water; color [xDBF5FF]; cpk 40%; display add selected;
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select ~ligand; cpk 40%; wireframe 0.3; color cpk;
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select temp;
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</script>
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</jmolButton>
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</jmol>
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3) Alternate rendering: <jmol>
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<jmolButton>
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<text>start</text>
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<script>
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/* alternate */
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select protein; color trace chain;
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select temp;
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refresh;
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delay 1.0;
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select protein; color trace none;
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select temp;
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refresh;
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loop 1.0;
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</script>
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</jmolButton>
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<jmolButton>
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<text>stop</text>
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<script>!quit;</script>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<text>Show just the site and ligand</text>
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<script>
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zoomTo 0.5 (~ligand, ~allosteric) 0; display (~ligand, ~allosteric);
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</script>
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</jmolButton>
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<jmolButton>
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<text>Cancel (show all)</text>
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<script>
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display all; zoomTo 0.5 (all) 0;
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</script>
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</jmolButton>
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</jmol>
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</StructureSection>

Current revision

Alternate rendering for display of both evolutionary conservation and allosteric site

This is a proof-of-concept.

Hemoglobin

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

Angel Herraez

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