Example Chimera Web Log File

This is a hand mock-up of proposed Chimera capability to automatically log analysis done in Chimera, including thumbnail images, numeric results and links to sessions, data files, movies, ....

The data file and this web page can be downloaded rsvdata.zip (110 Mbytes). The Chimera session files contain references to electron microscopy map files included in this download. The sessions were made with a Chimera 1.6 pre-release (April 2011).

Rous sarcoma virus capsid compared to HIV

Thu Apr 7 17:48 PDT 2011

Opened emd_1862.map (#0), size 255³, grid spacing 1.27 Å
contour level -363, minimum -17270, maximum 14818
mean -6649.5, sd 3176.6, rms 7369.3, 16-bit integer
computer generated image

Opened 1em9.pdb (#1), 2 chains A B, 2257 atoms, x-ray 2.05 Angstroms
rous sarcoma virus capsid protein: n-terminal domain
weight 30.04 KDa

Deleted 1091 atoms (chain B), 1em9.pdb (#1)

Opened 1eoq.pdb (#2), 1 chain A, 1209 atoms, NMR
rous sarcoma virus capsid protein: c-terminal domain
weight 8.497 KDa

5	Molecular weight 24.04 KDa, 2375 atoms (1em9.pdb (#1), 1eoq.pdb (#2)).

6	Contour level 1239, emd_1862.map (#0)

7	Enclosed volume 1.78e6 Å³, area 454.6e3 Å³, emd_1862.map (#0)

8	Note: Set contour level to enclose volume 60 * 24 KDa * 1.2 Å³/Da

Fit 1em9.pdb (#1) in emd_1862.map (#0)
correlation 0.7883, average density 4850, 173 of 1166 atoms outside contour
simulated map 10.4 Å, envelope 0.95 mass enclosed, optimized overlap

rock movie
session9.py

Segmented emd_1862.map (#0)
regions 360, smoothing steps 3, step size 1 voxel

Segmentation grouping emd_1862.map (#0)
regions 120, smoothing level 4 voxels

Fit to segment 1eoq.pdb (#2) in region 1966, emd_1862.seg (#3)
correlation 0.8737, masked to region
simulated map 10.4 Å, envelope 0.95 mass enclosed, optimized overlap

Spin movie 1em9.pdb (#1), 1eoq.pdb (#2), emd_1862.seg (#3)

spin session13.py

Combined 1em9.pdb (#1), 1eoq.pdb (#2) producing combination (#4)

15	Saved ca_fit.pdb (#4) relative to emd_1862.map (#0).

Symmetry copies ca_fit.pdb (#4) producing (#5.1-59)
icosahedral 222r, coordinate system emd_1862.map (#0).

Simulated map ca_fit.pdb (#4), (#5.1-59) producing molmap res 10.4 (#6)
resolution 10.4, grid spacing 1.27 Å

session17.py

18	Saved map ca_fit_60_r10.4.mrc (#6)

19	Measure correlation ca_fit_60_r10.4.mrc (#6), emd_1862.map (#0). corr 0.9403, corr about mean 0.6705, within contour level 0.19 (#6).

20	Resampled map ca_fit_60_r10.4.mrc (#6) on grid emd_1862.map (#0) producing (#7).

21	Saved map ca_fit.mrc (#7).

22	Shifted map emd_1862.map (#0) by 6649 producing (#9).

23	Scaled map (#9) by 2.63e-5 producing map (#10).

24	Saved map emd_1862_normal.mrc (#10)

Morph maps emd_1862_normal.mrc (#10) to ca_fit.mrc (#7)
producing map (#11).

morph25.mov

Difference map ca_fit.mrc (#7), emd_1862_normal.mrc (#10).
Minimum RMS scaling. Contours -0.19 blue, 0.19 red.

spin26.mov

Note: 2 pentamers

session26.py

Molecular surfaces ca_fit.pdb (#4), (#5.1)

rock28.mov

29	Buried area ca_fit.pdb (#4), (#5.1) solvent accessible area 486.4 Å², solvent excluded area 138.0 Å².

Buried residues ca_fit.pdb (#4), (#5.1)
11 residues, solvent accessible area cutoff 10 Å².
Total buried SAS area 303.0 Å², average 27.5 Å².

residue list

Opened 3p05.pdb (#12), x-ray 2.50 Angstroms
5 chains A B C D E, 7918 atoms, 1043 residues
pentameric hiv-1 ca
weight 105 KDa

Fit 3p05.pdb (#12) in emd_1862.map (#0)
correlation 0.53, average density 3548, 2160 of 7918 atoms outside contour
simulated map 10.4 Å, envelope 0.95 mass enclosed, optimized overlap

Note: Superposition of HIV and RSV pentamers.
HIV 3p05.pdb (light blue and pink)
RSV ca_fit.pdb (blue and red)
Helices align. HIV squeezed toward center.

spin32.mov
session32.py

Fri Apr 8 00:15 PDT 2011