Sandbox 5 Eric Martz: Difference between revisions
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<div style="background-color:#ffd8d8;border-width:1px;border-color:#b00000;border-style:solid;padding:5px;"> | <div style="background-color:#ffd8d8;border-width:1px;border-color:#b00000;border-style:solid;padding:5px;"> | ||
This page is reserved for Eric Martz and | This page is reserved for Eric Martz and Jaim Prilusky. | ||
</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}} {{Template:ColorKey_Element_Fe}}' | ||
scene='Sandbox_5_Eric_Martz/Heme/4' /> | |||
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 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 | |||
[[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/6'>Protein spacefilled</scene>. (Protein color key below) | |||
* <scene name='Sandbox_5_Eric_Martz/Heme/4'>Initial scene</scene> (heme only). | |||
{{Template:ColorKey_N2CRainbow}} | |||
==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. | |||
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) | |||
*set backgroundModel 11 | |||
*frame range 1 10 | |||
*frame play # must be used instead of "animation on" which resets the frame range to "all". | |||
Latest revision as of 21:34, 18 July 2010
This page is reserved for Eric Martz and Jaim Prilusky.
This is a 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 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 File:Hb heme morph.pdb.
- . (Protein color key below)
- . (Protein color key below)
- (heme only).
| N | C |
Jmol NotesJmol 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.
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)
- set backgroundModel 11
- frame range 1 10
- frame play # must be used instead of "animation on" which resets the frame range to "all".