User:Angel Herraez/Sandbox 3
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< User:Angel Herraez(Difference between revisions)
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| - | == | + | == Alternate rendering for display of both evolutionary conservation and allosteric site == |
| - | <scene | + | This is a proof-of-concept. |
| + | |||
| + | <StructureSection load='1b86' size='340' side='right' caption='Hemoglobin' scene=''> | ||
| + | === Hemoglobin with 2,3-BPG and oxygen === | ||
| + | |||
| + | As a reference: <scene name='38/388991/Default_rendering/3'>default Proteopedia rendering</scene> | ||
| + | |||
| + | 1) You must first apply <scene name='38/388991/Evolcons_rendering/1'>Proteopedia rendering for Evol.Cons.</scene> | ||
| + | |||
| + | 2) Then <jmol> | ||
| + | <jmolButton> | ||
| + | <text>get prepared</text> | ||
| + | <script> | ||
| + | /* define sites */ | ||
| + | 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; | ||
| + | define ~ligand [DG2]701:D; | ||
| + | /* common script */ | ||
| + | define temp selected; | ||
| + | select protein; trace -1.0; color trace chain; | ||
| + | select ~allosteric; cpk on; | ||
| + | select ~allosteric and water; color [xDBF5FF]; cpk 40%; display add selected; | ||
| + | select ~ligand; cpk 40%; wireframe 0.3; color cpk; | ||
| + | select temp; | ||
| + | </script> | ||
| + | </jmolButton> | ||
| + | </jmol> | ||
| + | |||
| + | 3) Alternate rendering: <jmol> | ||
| + | <jmolButton> | ||
| + | <text>start</text> | ||
| + | <script> | ||
| + | /* alternate */ | ||
| + | select protein; color trace chain; | ||
| + | select temp; | ||
| + | refresh; | ||
| + | delay 1.0; | ||
| + | select protein; color trace none; | ||
| + | select temp; | ||
| + | refresh; | ||
| + | loop 1.0; | ||
| + | </script> | ||
| + | </jmolButton> | ||
| + | |||
| + | <jmolButton> | ||
| + | <text>stop</text> | ||
| + | <script>!quit;</script> | ||
| + | </jmolButton> | ||
| + | </jmol> | ||
| + | |||
| + | |||
| + | |||
| + | <jmol> | ||
| + | <jmolButton> | ||
| + | <text>Show just the site and ligand</text> | ||
| + | <script> | ||
| + | zoomTo 0.5 (~ligand, ~allosteric) 0; display (~ligand, ~allosteric); | ||
| + | </script> | ||
| + | </jmolButton> | ||
| + | <jmolButton> | ||
| + | <text>Cancel (show all)</text> | ||
| + | <script> | ||
| + | display all; zoomTo 0.5 (all) 0; | ||
| + | </script> | ||
| + | </jmolButton> | ||
| + | </jmol> | ||
| + | |||
| + | </StructureSection> | ||
Current revision
Alternate rendering for display of both evolutionary conservation and allosteric site
This is a proof-of-concept.
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