Sandbox 5 Eric Martz: Difference between revisions
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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. | 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. | ||
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". | |||
Revision as of 02:57, 18 July 2010
This page is reserved for Eric Martz and Jaim Prilusky.
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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).
For more details about the morph PDB file: see File:Hb heme morph.pdb.
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.
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".