Sandbox 5 Eric Martz - Revision history

Eric Martz at 18:34, 18 July 2010

Eric Martz — Sun, 18 Jul 2010 18:34:40 GMT

←Older revision		Revision as of 18:34, 18 July 2010
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	[[Image:Hb_heme_morph.pdb]].		[[Image:Hb_heme_morph.pdb]].

		+	{{Template:Button Toggle Animation2}}
	* <scene name='Sandbox_5_Eric_Martz/Heme/5'>Protein as backbone trace</scene>. (Protein color key below)		* <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/6'>Protein spacefilled</scene>. (Protein color key below)

Eric Martz at 18:28, 18 July 2010

Eric Martz — Sun, 18 Jul 2010 18:28:12 GMT

←Older revision		Revision as of 18:28, 18 July 2010
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	</div>		</div>

-	<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}}'	+	<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' />

Eric Martz at 18:25, 18 July 2010

Eric Martz — Sun, 18 Jul 2010 18:25:44 GMT

←Older revision		Revision as of 18:25, 18 July 2010
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	</div>		</div>

-	<applet size='400' frame='true' align='right' caption='Human deoxy-hemoglobin ([[1hga]]) [[Morphs\|morphed]] to the oxy form ([[1hho]]). {{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}} '	+	<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}}'
	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>.	+	* <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>.	+	* <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==

Eric Martz at 18:21, 18 July 2010

Eric Martz — Sun, 18 Jul 2010 18:21:24 GMT

←Older revision		Revision as of 18:21, 18 July 2010
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	</div>		</div>

-	<applet size='400' frame='true' align='right' caption='Human deoxy-hemoglobin ([[1hga]]) [[Morphs\|morphed]] to the oxy form ([[1hho]]).'	+	<applet size='400' frame='true' align='right' caption='Human deoxy-hemoglobin ([[1hga]]) [[Morphs\|morphed]] to the oxy form ([[1hho]]). {{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}} '
	scene='Sandbox_5_Eric_Martz/Heme/4' />		scene='Sandbox_5_Eric_Martz/Heme/4' />

Eric Martz at 18:17, 18 July 2010

Eric Martz — Sun, 18 Jul 2010 18:17:48 GMT

←Older revision		Revision as of 18:17, 18 July 2010
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	</div>		</div>

-	<applet size='400' frame='true' align='right' caption='Human deoxy-hemoglobin ([[1hga]]) morphed to the oxy form ([[1hho]]).'	+	<applet size='400' frame='true' align='right' caption='Human deoxy-hemoglobin ([[1hga]]) [[Morphs\|morphed]] to the oxy form ([[1hho]]).'
	scene='Sandbox_5_Eric_Martz/Heme/4' />		scene='Sandbox_5_Eric_Martz/Heme/4' />

Eric Martz at 18:17, 18 July 2010

Eric Martz — Sun, 18 Jul 2010 18:17:12 GMT

←Older revision		Revision as of 18:17, 18 July 2010
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	</div>		</div>

-	<applet size='400' frame='true' align='right' caption='Human deoxy-hemoglobin [[1hga]] morphed to the oxy form ([[1hho]]).'	+	<applet size='400' frame='true' align='right' caption='Human deoxy-hemoglobin ([[1hga]]) morphed to the oxy form ([[1hho]]).'
	scene='Sandbox_5_Eric_Martz/Heme/4' />		scene='Sandbox_5_Eric_Martz/Heme/4' />

Eric Martz at 18:16, 18 July 2010

Eric Martz — Sun, 18 Jul 2010 18:16:30 GMT

←Older revision		Revision as of 18:16, 18 July 2010
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	</div>		</div>

-	<applet size='400' frame='true' align='right' caption='~~Insert caption here~~'	+	<applet size='400' frame='true' align='right' caption='Human deoxy-hemoglobin [[1hga]] morphed to the oxy form ([[1hho]]).'
	scene='Sandbox_5_Eric_Martz/Heme/4' />		scene='Sandbox_5_Eric_Martz/Heme/4' />

Eric Martz: /* Jmol Notes */

Eric Martz — Sun, 18 Jul 2010 18:09:20 GMT

Jmol Notes

←Older revision		Revision as of 18:09, 18 July 2010
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	==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)

Eric Martz at 18:08, 18 July 2010

Eric Martz — Sun, 18 Jul 2010 18:08:03 GMT

←Older revision		Revision as of 18:08, 18 July 2010
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	This is a [[Morphs#Linear_Interpolation\|linear interpolation morph]] showing the oxygenation/deoxygenation of heme in the beta chain of human hemoglobin. Chain B of [[1hga]] (deoxygenated, 2.1 Å) was morphed to chain B of [[1hho]] (oxygenated, 2.1 Å). The two chains were aligned on three carbon atoms in the heme.		This is a [[Morphs#Linear_Interpolation\|linear interpolation morph]] showing the oxygenation/deoxygenation of heme in the beta chain of human hemoglobin. Chain B of [[1hga]] (deoxygenated, 2.1 Å) was morphed to chain B of [[1hho]] (oxygenated, 2.1 Å). The two chains were aligned on three carbon atoms in the heme.

-	The two carboxy ~~atoms~~ on the heme, and one other carbon atom, were "frozen" because their positions in the two starting models differ for unimportant reasons, and their morph movements are distracting.	+	The two carboxy groups on the heme, and one other carbon atom, were "frozen" because their positions in the two starting models differ for unimportant reasons, and their morph movements are distracting.

	For more details about the morph PDB file: see		For more details about the morph PDB file: see

Eric Martz: /* Jmol Notes */

Eric Martz — Sun, 18 Jul 2010 00:33:01 GMT

Jmol Notes

←Older revision		Revision as of 00:33, 18 July 2010
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	==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 twohis". The iron-coordinating nitrogens in these his sidechains can be selected as "twohisn" or (his63.ne2,his92.ne2).	+	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)