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Update examples using latest IMP.
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- Add human-readable descriptions for each external file
  (populate ihm_external_files.details). Closes #35.
- Split the Nup84 archive into multiple smaller files, so that
  downloading the more frequently used files is much faster.
  Closes #25.
- Repack Nup84 ensembles so they're not double compressed. Relates #24.
- Link to alignment files where available for the Nup84 example.
  Closes #16.
- Add transformation and cross correlation that fits each Nup84 model
  onto the 2D EM class average. Closes #30.
- Convert the Nup84 2D EM class average from the rather rare text
  PGM format into binary PGM. Closes #33.
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@benmwebb
benmwebb committed May 17, 2017
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26 changes: 17 additions & 9 deletions examples/exosome/exosome.cif
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Expand Up @@ -5851,20 +5851,28 @@ _ihm_external_files.reference_id
_ihm_external_files.file_path
_ihm_external_files.content_type
_ihm_external_files.details
1 1 cluster.0/Rrp46_gfp.mrc 'Modeling or post-processing output' .
2 1 cluster.0/Lrp1.mrc 'Modeling or post-processing output' .
3 1 cluster.0/Rrp6.mrc 'Modeling or post-processing output' .
4 1 cluster.0/MPP6.mrc 'Modeling or post-processing output' .
5 2 cluster.1/Rrp46_gfp.mrc 'Modeling or post-processing output' .
6 2 cluster.1/Lrp1.mrc 'Modeling or post-processing output' .
7 2 cluster.1/Rrp6.mrc 'Modeling or post-processing output' .
8 2 cluster.1/MPP6.mrc 'Modeling or post-processing output' .
1 1 cluster.0/Rrp46_gfp.mrc 'Modeling or post-processing output'
'Localization density for Rrp46_gfp'
2 1 cluster.0/Lrp1.mrc 'Modeling or post-processing output'
'Localization density for Lrp1'
3 1 cluster.0/Rrp6.mrc 'Modeling or post-processing output'
'Localization density for Rrp6'
4 1 cluster.0/MPP6.mrc 'Modeling or post-processing output'
'Localization density for MPP6'
5 2 cluster.1/Rrp46_gfp.mrc 'Modeling or post-processing output'
'Localization density for Rrp46_gfp'
6 2 cluster.1/Lrp1.mrc 'Modeling or post-processing output'
'Localization density for Lrp1'
7 2 cluster.1/Rrp6.mrc 'Modeling or post-processing output'
'Localization density for Rrp6'
8 2 cluster.1/MPP6.mrc 'Modeling or post-processing output'
'Localization density for MPP6'
9 3 exosome-v1.0/modeling-scripts_Rrp6.1/exosome.modeling.py
'Modeling workflow or script' 'The main integrative modeling script'
10 3 exosome-v1.0/Rrp6.analysis/clustering.py 'Modeling workflow or script'
'Main clustering and analysis script'
11 3 exosome-v1.0/data/exosome_XLMS_column07012014.csv
'Input data or restraints' .
'Input data or restraints' Crosslinks
#
#
loop_
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260 changes: 172 additions & 88 deletions examples/mediator/mediator.cif
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Expand Up @@ -9631,95 +9631,179 @@ _ihm_external_files.reference_id
_ihm_external_files.file_path
_ihm_external_files.content_type
_ihm_external_files.details
1 1 cluster.0/med6.mrc 'Modeling or post-processing output' .
2 1 cluster.0/med8.mrc 'Modeling or post-processing output' .
3 1 cluster.0/med11.mrc 'Modeling or post-processing output' .
4 1 cluster.0/med17.mrc 'Modeling or post-processing output' .
5 1 cluster.0/med18.mrc 'Modeling or post-processing output' .
6 1 cluster.0/med20.mrc 'Modeling or post-processing output' .
7 1 cluster.0/med22.mrc 'Modeling or post-processing output' .
8 1 cluster.0/med4.mrc 'Modeling or post-processing output' .
9 1 cluster.0/med7.mrc 'Modeling or post-processing output' .
10 1 cluster.0/med9.mrc 'Modeling or post-processing output' .
11 1 cluster.0/med31.mrc 'Modeling or post-processing output' .
12 1 cluster.0/med21.mrc 'Modeling or post-processing output' .
13 1 cluster.0/med10.mrc 'Modeling or post-processing output' .
14 1 cluster.0/med1.mrc 'Modeling or post-processing output' .
15 1 cluster.0/med14.mrc 'Modeling or post-processing output' .
16 1 cluster.0/med19.mrc 'Modeling or post-processing output' .
17 1 cluster.0/med2.mrc 'Modeling or post-processing output' .
18 1 cluster.0/med3.mrc 'Modeling or post-processing output' .
19 1 cluster.0/med5.mrc 'Modeling or post-processing output' .
20 1 cluster.0/med15.mrc 'Modeling or post-processing output' .
21 1 cluster.0/med16.mrc 'Modeling or post-processing output' .
22 2 cluster.1/med6.mrc 'Modeling or post-processing output' .
23 2 cluster.1/med8.mrc 'Modeling or post-processing output' .
24 2 cluster.1/med11.mrc 'Modeling or post-processing output' .
25 2 cluster.1/med17.mrc 'Modeling or post-processing output' .
26 2 cluster.1/med18.mrc 'Modeling or post-processing output' .
27 2 cluster.1/med20.mrc 'Modeling or post-processing output' .
28 2 cluster.1/med22.mrc 'Modeling or post-processing output' .
29 2 cluster.1/med4.mrc 'Modeling or post-processing output' .
30 2 cluster.1/med7.mrc 'Modeling or post-processing output' .
31 2 cluster.1/med9.mrc 'Modeling or post-processing output' .
32 2 cluster.1/med31.mrc 'Modeling or post-processing output' .
33 2 cluster.1/med21.mrc 'Modeling or post-processing output' .
34 2 cluster.1/med10.mrc 'Modeling or post-processing output' .
35 2 cluster.1/med1.mrc 'Modeling or post-processing output' .
36 2 cluster.1/med14.mrc 'Modeling or post-processing output' .
37 2 cluster.1/med19.mrc 'Modeling or post-processing output' .
38 2 cluster.1/med2.mrc 'Modeling or post-processing output' .
39 2 cluster.1/med3.mrc 'Modeling or post-processing output' .
40 2 cluster.1/med5.mrc 'Modeling or post-processing output' .
41 2 cluster.1/med15.mrc 'Modeling or post-processing output' .
42 2 cluster.1/med16.mrc 'Modeling or post-processing output' .
43 3 cluster.2/med6.mrc 'Modeling or post-processing output' .
44 3 cluster.2/med8.mrc 'Modeling or post-processing output' .
45 3 cluster.2/med11.mrc 'Modeling or post-processing output' .
46 3 cluster.2/med17.mrc 'Modeling or post-processing output' .
47 3 cluster.2/med18.mrc 'Modeling or post-processing output' .
48 3 cluster.2/med20.mrc 'Modeling or post-processing output' .
49 3 cluster.2/med22.mrc 'Modeling or post-processing output' .
50 3 cluster.2/med4.mrc 'Modeling or post-processing output' .
51 3 cluster.2/med7.mrc 'Modeling or post-processing output' .
52 3 cluster.2/med9.mrc 'Modeling or post-processing output' .
53 3 cluster.2/med31.mrc 'Modeling or post-processing output' .
54 3 cluster.2/med21.mrc 'Modeling or post-processing output' .
55 3 cluster.2/med10.mrc 'Modeling or post-processing output' .
56 3 cluster.2/med1.mrc 'Modeling or post-processing output' .
57 3 cluster.2/med14.mrc 'Modeling or post-processing output' .
58 3 cluster.2/med19.mrc 'Modeling or post-processing output' .
59 3 cluster.2/med2.mrc 'Modeling or post-processing output' .
60 3 cluster.2/med3.mrc 'Modeling or post-processing output' .
61 3 cluster.2/med5.mrc 'Modeling or post-processing output' .
62 3 cluster.2/med15.mrc 'Modeling or post-processing output' .
63 3 cluster.2/med16.mrc 'Modeling or post-processing output' .
64 4 cluster.3/med6.mrc 'Modeling or post-processing output' .
65 4 cluster.3/med8.mrc 'Modeling or post-processing output' .
66 4 cluster.3/med11.mrc 'Modeling or post-processing output' .
67 4 cluster.3/med17.mrc 'Modeling or post-processing output' .
68 4 cluster.3/med18.mrc 'Modeling or post-processing output' .
69 4 cluster.3/med20.mrc 'Modeling or post-processing output' .
70 4 cluster.3/med22.mrc 'Modeling or post-processing output' .
71 4 cluster.3/med4.mrc 'Modeling or post-processing output' .
72 4 cluster.3/med7.mrc 'Modeling or post-processing output' .
73 4 cluster.3/med9.mrc 'Modeling or post-processing output' .
74 4 cluster.3/med31.mrc 'Modeling or post-processing output' .
75 4 cluster.3/med21.mrc 'Modeling or post-processing output' .
76 4 cluster.3/med10.mrc 'Modeling or post-processing output' .
77 4 cluster.3/med1.mrc 'Modeling or post-processing output' .
78 4 cluster.3/med14.mrc 'Modeling or post-processing output' .
79 4 cluster.3/med19.mrc 'Modeling or post-processing output' .
80 4 cluster.3/med2.mrc 'Modeling or post-processing output' .
81 4 cluster.3/med3.mrc 'Modeling or post-processing output' .
82 4 cluster.3/med5.mrc 'Modeling or post-processing output' .
83 4 cluster.3/med15.mrc 'Modeling or post-processing output' .
84 4 cluster.3/med16.mrc 'Modeling or post-processing output' .
1 1 cluster.0/med6.mrc 'Modeling or post-processing output'
'Localization density for med6'
2 1 cluster.0/med8.mrc 'Modeling or post-processing output'
'Localization density for med8'
3 1 cluster.0/med11.mrc 'Modeling or post-processing output'
'Localization density for med11'
4 1 cluster.0/med17.mrc 'Modeling or post-processing output'
'Localization density for med17'
5 1 cluster.0/med18.mrc 'Modeling or post-processing output'
'Localization density for med18'
6 1 cluster.0/med20.mrc 'Modeling or post-processing output'
'Localization density for med20'
7 1 cluster.0/med22.mrc 'Modeling or post-processing output'
'Localization density for med22'
8 1 cluster.0/med4.mrc 'Modeling or post-processing output'
'Localization density for med4'
9 1 cluster.0/med7.mrc 'Modeling or post-processing output'
'Localization density for med7'
10 1 cluster.0/med9.mrc 'Modeling or post-processing output'
'Localization density for med9'
11 1 cluster.0/med31.mrc 'Modeling or post-processing output'
'Localization density for med31'
12 1 cluster.0/med21.mrc 'Modeling or post-processing output'
'Localization density for med21'
13 1 cluster.0/med10.mrc 'Modeling or post-processing output'
'Localization density for med10'
14 1 cluster.0/med1.mrc 'Modeling or post-processing output'
'Localization density for med1'
15 1 cluster.0/med14.mrc 'Modeling or post-processing output'
'Localization density for med14'
16 1 cluster.0/med19.mrc 'Modeling or post-processing output'
'Localization density for med19'
17 1 cluster.0/med2.mrc 'Modeling or post-processing output'
'Localization density for med2'
18 1 cluster.0/med3.mrc 'Modeling or post-processing output'
'Localization density for med3'
19 1 cluster.0/med5.mrc 'Modeling or post-processing output'
'Localization density for med5'
20 1 cluster.0/med15.mrc 'Modeling or post-processing output'
'Localization density for med15'
21 1 cluster.0/med16.mrc 'Modeling or post-processing output'
'Localization density for med16'
22 2 cluster.1/med6.mrc 'Modeling or post-processing output'
'Localization density for med6'
23 2 cluster.1/med8.mrc 'Modeling or post-processing output'
'Localization density for med8'
24 2 cluster.1/med11.mrc 'Modeling or post-processing output'
'Localization density for med11'
25 2 cluster.1/med17.mrc 'Modeling or post-processing output'
'Localization density for med17'
26 2 cluster.1/med18.mrc 'Modeling or post-processing output'
'Localization density for med18'
27 2 cluster.1/med20.mrc 'Modeling or post-processing output'
'Localization density for med20'
28 2 cluster.1/med22.mrc 'Modeling or post-processing output'
'Localization density for med22'
29 2 cluster.1/med4.mrc 'Modeling or post-processing output'
'Localization density for med4'
30 2 cluster.1/med7.mrc 'Modeling or post-processing output'
'Localization density for med7'
31 2 cluster.1/med9.mrc 'Modeling or post-processing output'
'Localization density for med9'
32 2 cluster.1/med31.mrc 'Modeling or post-processing output'
'Localization density for med31'
33 2 cluster.1/med21.mrc 'Modeling or post-processing output'
'Localization density for med21'
34 2 cluster.1/med10.mrc 'Modeling or post-processing output'
'Localization density for med10'
35 2 cluster.1/med1.mrc 'Modeling or post-processing output'
'Localization density for med1'
36 2 cluster.1/med14.mrc 'Modeling or post-processing output'
'Localization density for med14'
37 2 cluster.1/med19.mrc 'Modeling or post-processing output'
'Localization density for med19'
38 2 cluster.1/med2.mrc 'Modeling or post-processing output'
'Localization density for med2'
39 2 cluster.1/med3.mrc 'Modeling or post-processing output'
'Localization density for med3'
40 2 cluster.1/med5.mrc 'Modeling or post-processing output'
'Localization density for med5'
41 2 cluster.1/med15.mrc 'Modeling or post-processing output'
'Localization density for med15'
42 2 cluster.1/med16.mrc 'Modeling or post-processing output'
'Localization density for med16'
43 3 cluster.2/med6.mrc 'Modeling or post-processing output'
'Localization density for med6'
44 3 cluster.2/med8.mrc 'Modeling or post-processing output'
'Localization density for med8'
45 3 cluster.2/med11.mrc 'Modeling or post-processing output'
'Localization density for med11'
46 3 cluster.2/med17.mrc 'Modeling or post-processing output'
'Localization density for med17'
47 3 cluster.2/med18.mrc 'Modeling or post-processing output'
'Localization density for med18'
48 3 cluster.2/med20.mrc 'Modeling or post-processing output'
'Localization density for med20'
49 3 cluster.2/med22.mrc 'Modeling or post-processing output'
'Localization density for med22'
50 3 cluster.2/med4.mrc 'Modeling or post-processing output'
'Localization density for med4'
51 3 cluster.2/med7.mrc 'Modeling or post-processing output'
'Localization density for med7'
52 3 cluster.2/med9.mrc 'Modeling or post-processing output'
'Localization density for med9'
53 3 cluster.2/med31.mrc 'Modeling or post-processing output'
'Localization density for med31'
54 3 cluster.2/med21.mrc 'Modeling or post-processing output'
'Localization density for med21'
55 3 cluster.2/med10.mrc 'Modeling or post-processing output'
'Localization density for med10'
56 3 cluster.2/med1.mrc 'Modeling or post-processing output'
'Localization density for med1'
57 3 cluster.2/med14.mrc 'Modeling or post-processing output'
'Localization density for med14'
58 3 cluster.2/med19.mrc 'Modeling or post-processing output'
'Localization density for med19'
59 3 cluster.2/med2.mrc 'Modeling or post-processing output'
'Localization density for med2'
60 3 cluster.2/med3.mrc 'Modeling or post-processing output'
'Localization density for med3'
61 3 cluster.2/med5.mrc 'Modeling or post-processing output'
'Localization density for med5'
62 3 cluster.2/med15.mrc 'Modeling or post-processing output'
'Localization density for med15'
63 3 cluster.2/med16.mrc 'Modeling or post-processing output'
'Localization density for med16'
64 4 cluster.3/med6.mrc 'Modeling or post-processing output'
'Localization density for med6'
65 4 cluster.3/med8.mrc 'Modeling or post-processing output'
'Localization density for med8'
66 4 cluster.3/med11.mrc 'Modeling or post-processing output'
'Localization density for med11'
67 4 cluster.3/med17.mrc 'Modeling or post-processing output'
'Localization density for med17'
68 4 cluster.3/med18.mrc 'Modeling or post-processing output'
'Localization density for med18'
69 4 cluster.3/med20.mrc 'Modeling or post-processing output'
'Localization density for med20'
70 4 cluster.3/med22.mrc 'Modeling or post-processing output'
'Localization density for med22'
71 4 cluster.3/med4.mrc 'Modeling or post-processing output'
'Localization density for med4'
72 4 cluster.3/med7.mrc 'Modeling or post-processing output'
'Localization density for med7'
73 4 cluster.3/med9.mrc 'Modeling or post-processing output'
'Localization density for med9'
74 4 cluster.3/med31.mrc 'Modeling or post-processing output'
'Localization density for med31'
75 4 cluster.3/med21.mrc 'Modeling or post-processing output'
'Localization density for med21'
76 4 cluster.3/med10.mrc 'Modeling or post-processing output'
'Localization density for med10'
77 4 cluster.3/med1.mrc 'Modeling or post-processing output'
'Localization density for med1'
78 4 cluster.3/med14.mrc 'Modeling or post-processing output'
'Localization density for med14'
79 4 cluster.3/med19.mrc 'Modeling or post-processing output'
'Localization density for med19'
80 4 cluster.3/med2.mrc 'Modeling or post-processing output'
'Localization density for med2'
81 4 cluster.3/med3.mrc 'Modeling or post-processing output'
'Localization density for med3'
82 4 cluster.3/med5.mrc 'Modeling or post-processing output'
'Localization density for med5'
83 4 cluster.3/med15.mrc 'Modeling or post-processing output'
'Localization density for med15'
84 4 cluster.3/med16.mrc 'Modeling or post-processing output'
'Localization density for med16'
85 5 mediator-v1.0.2/sampling/modeling/modeling.py 'Modeling workflow or script'
'The main integrative modeling script'
86 5 mediator-v1.0.2/analysis/clustering/clustering.py
'Modeling workflow or script' 'Main clustering and analysis script'
87 6 . 'Input data or restraints' .
87 6 . 'Input data or restraints' 'Starting comparative model structure'
88 5 mediator-v1.0.2/sampling/pdb_files/med4_med9.pdb 'Input data or restraints'
'MED4 AND MED9 STRUCTURE TAKEN FROM LARIVIERE ET AL, NUCLEIC ACIDS RESEARCH. 2013;41:9266-9273. DOI: 10.1093/nar/gkt704. THE MED10 STRUCTURE ALSO PROPOSED IN THAT WORK IS NOT USED IN THIS STUDY.'
89 5 mediator-v1.0.2/sampling/pdb_files/med7n_med31.pdb
Expand All @@ -9729,9 +9813,9 @@ _ihm_external_files.details
'Input data or restraints'
'MED7C AND MED21 STRUCTURES FROM PDB ENTRY 1YKH, ROTATED AND TRANSLATED TO ALIGN WITH THE MED4-MED9 MODEL'
91 5 mediator-v1.0.2/sampling/pdb_files/med16.NTD.phyre.model.pdb
'Input data or restraints' .
'Input data or restraints' 'Starting model structure'
92 5 mediator-v1.0.2/sampling/CXMS_files/full_med_splitmods.txt
'Input data or restraints' .
'Input data or restraints' Crosslinks
93 5
mediator-v1.0.2/sampling/em_map_files/asturias_middle_module_translated_resampled.mrc
'Input data or restraints' 'Original MRC file from which the GMM was derived'
Expand Down Expand Up @@ -21351,7 +21435,7 @@ _ihm_starting_comparative_models.template_sequence_identity
_ihm_starting_comparative_models.template_sequence_identity_denominator
_ihm_starting_comparative_models.template_dataset_list_id
_ihm_starting_comparative_models.alignment_file_id
1 med16-m1 A 8 538 A 13 334 11 1 8 .
1 med16-m1 A 8 538 A 13 334 11 1 8 ?
#
#
loop_
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