Task
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Input files (click on filename) |
Output (click
on image or text)
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The crystal structure
of Pyrobaculum
aerophilum
(Pae) SurEα
reveals a dimer in the asymmetric unit of a P3(1)21 cell. We
want a simple ribbon diagram of the dimer, as viewed down the NCS 2-fold. |
PaeSurE_simple_ribbons.pml
[PyMOL script file with some descriptive comments]
PaeSurE_dimer.pdb
[PDB file in which SeMet's have been changed to
MET, because I was too lazy to have PyMOL properly deal with METs] |
PaeSurE_simple_ribbons.png |
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The crystal structure
of Pyrobaculum
aerophilum
(Pae) SmAP1 reveals a
heptamer in the asymmetric unit of a C222(1) cell. A 14-mer is created
by one of the crystallographic 2-folds. We
want to display a ribbon diagram of the 14-mer, clearly illustrating the
surface area that's buried in the
heptamer···heptamer interface.
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PaeSmAP1_14mer_interface.pml
[PyMOL script file with
lots of descriptive comments]
gpa14mer_buriedsurface.pdb
[PDB-format file with modified B-factors that
describe whether the atom is part of the interface (B>0) or not (B=0)]
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PaeSmAP1_14mer_interface.png
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The crystal structure
of Methanobacterium thermautotropicum
(Mth) SmAP1 reveals a 14-mer in
the asymmetric unit of a P2(1) cell. Several ligands (such as UMP, MPD, etc.) are bound to this 14-mer. We want to display a ribbon diagram of
the 14-mer viewed down the 7-fold axis, illustrating the protein as
ribbons and the ligands as color-coded CPK spheres. |
MthSmAP1_ribbons_and_ligands.pml
[PyMOL script file]
mth_p21.pdb
[PDB file for final, refined structure] |
MthSmAP1_ribbons_and_ligands.png |
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The crystal structure
of Pyrobaculum
aerophilum
(Pae) SurEα
reveals a dimer in the asymmetric unit of a P3(1)21 cell. We want a figure of two types of
electron density, centered on Ser99 from chain 'B': 2Fo-Fc electron
density and experimentally-phased (MAD) density maps. One PyMOL script
produces both maps as separate panels (overlaying them in one panel is
messy). |
PaeSurE_densities_Ser99.pml
[PyMOL script file with some descriptive comments]
PaeSurE_fordensity.pdb
[PDB file in which SeMet's have been changed to
MET, because I was too lazy to have PyMOL properly deal with METs]
dm_phex20_ncs.xplor
[XPLOR map file calculated with experimental/MAD
phases]
map2fofc_nonds.xplor
[XPLOR 2Fo-Fc map calculated from model phases]
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PaeSurE_2fofc_Ser99.png PaeSurE_Fobs_Ser99.png |
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The crystal structure
of Mth SmAP1 reveals a 14-mer in
the asymmetric unit of a P2(1) cell. Several ligands (such as UMP, MPD, etc.) are bound to this 14-mer. We want to display the 14-mer and one
of its 14 MPD-binding sites, showing: (i) Mth SmAP1 as sticks; (ii) electron
density for MPD and proximal SmAP1 residues; (iii) distances between MPD····protein contacts (e.g., H-bonds). |
MthSmAP1_MPD_density.pml
[PyMOL script file with some descriptive comments]
mth_p21_ump.pdb
[PDB file containing Mth 14-mer, waters, MPDs,
UMPs, uridines, etc.]
mth_map2fofc.xplor
[XPLOR map file calculated with 2Fo-Fc coefficients]
mth_mapfofc.xplor
[XPLOR map file calculated with
Fo-Fc coefficients] |
MthSmAP1_MPD_density.png |
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The crystal structure
of Pae SurEα
reveals a dimer in the asymmetric unit of a P3(1)21 cell. We
want to render one of the monomers as a ribbon diagram and make a movie
of it spinning about the y-axis. This animation uses frames which are
anti-aliased and ray-traced, so the size can get outta hand. |
Icannotfindit.sorry
[...but visit the PyMOL manual; movies are easy.] |
PaeSurE_movie.gif |
