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last update: July 28, 2020
Info | Results |
Identify metrics most suitable for evaluating and comparing fit of atomic coordinate models into cryo-EM maps for specimens in the 1.5-4.0 Å reported overall resolution range.
Specific metrics for review:
There are two target specimens for this challenge.
Target Map Download: You can use this rsync script. Alternatively, you can download individual maps from EMDR atlas pages (click on EMDB id in the table below, select "download" tab).
T0101. Human Apoferritin |
T0102. Human Apoferritin |
T0103. Human Apoferritin |
T0104. Horse Liver Alcohol Dehydrogenase |
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target |
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EMDB entry Reported Resolution (Å) |
EMD-20026 |
EMD-20027 2.3 |
EMD-20028 3.1 |
EMD-0406 2.9 |
Sharpened/Masked map | emd_20026.map | emd_20027.map | emd_20028.map | emd_0406.map |
Unsharpened/Unmasked map | emd_20026_additional_2.map | emd_20027_additional_1.map | emd_20028_additional_1.map |
emd_0406_additional.map |
Single protomer map Identifies required position for chain A in submitted models |
emd_20026_additional_1.map | emd_20027_additional_2.map | emd_20028_additional_2.map |
n/a |
Half-maps | emd_20026_half_map_1.map, emd_20026_half_map_2.map | emd_20027_half_map_1.map, emd_20027_half_map_1.map | emd_20028_half_map_1.map, emd_20028_half_map_2.map |
emd_0406_half_map_1.map, emd_0406_half_map_2.map |
Primary Citation |
unpublished |
Herzik et al, 2019 | ||
Reference Models models in bold will be used as references in analysis pipeline |
3ajo (Xray) 2fha (Xray) |
6nbb (EM) 2jhf (Xray) |
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Imposed Map Symmetry |
Octahedral (O) |
Cyclic (C2) | ||
Specimen MW |
21 kDa x 24-fold = 504 kDa | 40 kDa x 2-fold = 80 kDa | ||
Map Contributors |
Kaiming Zhang, Greg Pintilie, Shanshan Li, Wah Chiu |
Mark Herzik, Mengyu Wu, Gabe Lander |
Human heavy chain Apoferritin (#1-3) Deposit: Single subunit, chain A, with position given by single protomer map Chain residue numbering starts with 1 Clarification: T=1, T=2, A=3, S=4, T=5, S=6, etc. Symmetry Matrices (center at x=y=z=109.2 Angstroms) |
Full Sequence (Uniprot P02794) TTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRI FLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGA PESGLAEYLFDKHTLGDSDNES |
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Horse liver Alcohol Dehydrogenase (#4) Deposit: either single subunit (Chain A) or Dimer (chains A and B). Chain positions same as 6nbb Chain residue numbering starts with 1 Clarification: S=1, T=2, A=3, S=4, G=5, K=6, etc. For associated ligand NAD, use same chain id as protein, residue#=401 Symmetry Matrices (2-fold at x=y=142.976 Angstroms) |
Full Sequence (Uniprot P00327) STAGKVIKCKAAVLWEEKKPFSIEEVEVAPPKAHEVRIKMVATGICRSDDHVVSGTLVTPLPVIAGHEAAGIVESIGEGV TTVRPGDKVIPLFTPQCGKCRVCKHPEGNFCLKNDLSMPRGTMQDGTSRFTCRGKPIHHFLGTSTFSQYTVVDEISVAKI DAASPLEKVCLIGCGFSTGYGSAVKVAKVTQGSTCAVFGLGGVGLSVIMGCKAAGAARIIGVDINKDKFAKAKEVGATEC VNPQDYKKPIQEVLTEMSNGGVDFSFEVIGRLDTMVTALSCCQEAYGVSVIVGVPPDSQNLSMNPMLLLSGRTWKGAIFG GFKSKDSVPKLVADFMAKKFALDPLITHVLPFEKINEGFDLLRSGESIRTILTF |
17 April | Open Challenge |
26 April, 11 AM US ET | Participant Teleconference |
1 May | Deposition form opens to collect participant models |
25 May 28 May (3 PM US ET) | Deadline for depositing models |
27 May 29 May | Deposited models and metadata made available for assessment (blinded) |
6 June | Results of model-compare pipeline made available |
13-15 June | Participant/Assessor Face-to-Face Meeting |
Q1: Alcohol Dehydrogenase Target: Why are the half-maps (512x512x512) so much larger than the primary deposited map (368x368x368) for EMD-0406? Answered by Mark Herzik: The half maps are unfiltered and completely unmodified from RELION’s output. We did not think it was necessary for purveyors of the EMDB to download a ~0.5 GB map of alcohol dehydrogenase when most of the voxels (512x512x512 box size) would be just averaged noise. We used the larger box size during processing, despite the small mass of ADH, to prevent aliasing and CTF delocalization issues. It’s unclear what is the established recommendations in this regard but we think it makes things easier for the user.
Q2: It seems that the half-maps for EMD-20026 (1.8 Å) are better than the full maps based on CC values to a docked model (same model for all maps) [the other apoferritin entries have better CC value for full map vs half-map]. Digest of subsequent discussion provided here.
Q3: Will fully automated models be accepted or should we go through and correct errors? In the challenge phase we want to collect "close to final" models (with errors identified/fixed as much as possible).
Q4: What is the goal of this challenge? For challengers, it is to build the best quality model possible given the map data. For assessors, it is to decide what metrics are best for comparing models.
Q5: Should we develop new methods for this challenge? We anticipate that everyone will make use of existing methods for modelling and assessment in this "short-timeline" round.
Q6: How many models can a modelling team submit? There is no limitation. Teams may submit multiple models per map.
Q7: What buffer was used to prepare the apoferritin sample? Answered by Kaiming Zhang (May 14): 50 mM TrisHCl, pH 7.5, 150 mM NaCl.
Q8: How can I access the single protomer map to find the reference position for chain A (apoferritin target)? (added May 21). The file name of the "additional" single protomer map included with the EMDB entry is listed in the target table.
Q9: Why are we asked to only submit a single chain model for the apoferritin targets? (added May 26). This simplifies analysis. We will be able to create/analyze full complexes in a consistent way across all submissions using the symmetry matrices provided in the instructions.
Q10: Can you tell me my modeller group id? These will be revealed near the end of the face-to-face meeting and posted here.
EMDataResource Validation Challenges are supported by NIH National Institute of General Medical Sciences
Please send your challenge questions, comments and feedback to challenges@emdataresource.org
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