Sandbox 5 Eric Martz: Difference between revisions
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</div> | </div> | ||
<applet size='400' frame='true' align='right' caption=' | <applet size='400' frame='true' align='right' caption='Human deoxy-hemoglobin ([[1hga]]) [[Morphs|morphed]] to the oxy form ([[1hho]]). Element colors: {{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}} {{Template:ColorKey_Element_Fe}}' | ||
scene='Sandbox_5_Eric_Martz/Heme/4' /> | scene='Sandbox_5_Eric_Martz/Heme/4' /> | ||
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[[Image:Hb_heme_morph.pdb]]. | [[Image:Hb_heme_morph.pdb]]. | ||
* <scene name='Sandbox_5_Eric_Martz/Heme/5'>Protein as backbone trace</scene>. | {{Template:Button Toggle Animation2}} | ||
* <scene name='Sandbox_5_Eric_Martz/Heme/6'>Protein spacefilled</scene>. | * <scene name='Sandbox_5_Eric_Martz/Heme/5'>Protein as backbone trace</scene>. (Protein color key below) | ||
* <scene name='Sandbox_5_Eric_Martz/Heme/6'>Protein spacefilled</scene>. (Protein color key below) | |||
* <scene name='Sandbox_5_Eric_Martz/Heme/4'>Initial scene</scene> (heme only). | * <scene name='Sandbox_5_Eric_Martz/Heme/4'>Initial scene</scene> (heme only). | ||
{{Template:ColorKey_N2CRainbow}} | |||
==Jmol Notes== | ==Jmol Notes== | ||
There are some formatting problems in this PDB file. Select iron with "hem.fe" (10 atoms, one in each model) and molecular oxygen with "hem.o?" (2 atoms, model 10 only). Iron is not recognized as such by Jmol and needed to be colored E06633. The two his sidechains shown are his62 and his92. Those sidechains can be selected with "select sidechain and (his63,his92)" or "select twohis". The iron-coordinating nitrogens in these his sidechains can be selected as "twohisn" or (his63.ne2,his92.ne2). Hmmm, it seems the SAT is destroying the defined tokens twohis and twohisn in the saved state scripts. Those worked prior to saving. | There are some formatting problems in this PDB file. Select iron with "hem.fe" (10 atoms, one in each model) and molecular oxygen with "hem.o?" (2 atoms, model 10 only). Iron is not recognized as such by Jmol and needed to be colored E06633. The two his sidechains shown are his62 and his92. Those sidechains can be selected with "select sidechain and (his63,his92)" or "select twohis". The iron-coordinating nitrogens in these his sidechains can be selected as "twohisn" or (his63.ne2,his92.ne2). Hmmm, it seems the [[SAT]] is destroying the defined tokens twohis and twohisn in the saved state scripts. Those worked prior to saving. | ||
If the last two atoms in the PDB file (molecular oxygen) were copied into a MODEL 11, they could be shown translucent throughout the animation, becoming opaque only in model 10. The script would need to include something like this (untested) | If the last two atoms in the PDB file (molecular oxygen) were copied into a MODEL 11, they could be shown translucent throughout the animation, becoming opaque only in model 10. The script would need to include something like this (untested) | ||