# 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

1 | 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 |

2 | 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 |

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

4 | 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

9 | 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

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

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

12 | 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 |

13 | Spin movie 1em9.pdb (#1), 1eoq.pdb (#2), emd_1862.seg (#3) |  | spin session13.py

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

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

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

17 | 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)

25 | Morph maps emd_1862_normal.mrc (#10) to ca_fit.mrc (#7) producing map (#11). |  | morph25.mov

26 | Difference map ca_fit.mrc (#7), emd_1862_normal.mrc (#10). Minimum RMS scaling. Contours -0.19 blue, 0.19 red. |  | spin26.mov

27 | Note: 2 pentamers |  | session26.py

28 | 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.

29 | 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

30 | 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 |

31 | 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 |

32 | 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