Ab initio model datasets » History » Version 1
Sargis Dallakyan, 04/07/2015 08:46 PM
| 1 | 1 | Sargis Dallakyan | h1. Ab initio model datasets of 50S ribosomal subunit |
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| 3 | h2. Information |
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| 5 | These datasets were used to support various _Ab initio_ reconstruction procedures as described in ("Voss _et al._ 2010":http://www.ncbi.nlm.nih.gov/pubmed/20018246). |
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| 7 | The experiments included are: YYmonDDa etc., where YY refers to the year, mon to the month and DD to the day of data acquisition. a, b, c, etc. are subsequent experiments on that day. |
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| 9 | Original images may be viewed using the "Leginon image viewer":http://emportal.nysbc.org/myamiweb/imageviewer.php?expId=6592 and downloaded one-by-one from the Leginon viewer or as an entire set using the [[Dbemwiz|dbemwiz.jar]] tool and selecting the experiment, named as YYmonDDa. |
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| 10 | Summary information may be viewed using the Leginon summary pages and processed data may be examined using the [[appion:|Appion processing pipeline]]. Images and metadata may be downloaded from these websites or using the links below. |
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| 12 | h2. List of available datasets: |
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| 14 | table{border:1px solid black}. |
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| 15 | {background:#ddd}. |Session Name|Leginon Description| |
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| 16 | | "09apr14b":http://emportal.nysbc.org/myamiweb/imageviewer.php?expId=6592 | 50S Ribosome subunit, vitreous ice, 100k particles | |
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| 17 | | "09mar04b":http://emportal.nysbc.org/myamiweb/imageviewer.php?expId=6498 | 50S Ribosome subunit, vitreous ice, Pt Coated C_Flats | |
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| 18 | | "09feb18c":http://emportal.nysbc.org/myamiweb/imageviewer.php?expId=6453 | 50S Ribosome subunit, tomography | |
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| 19 | | "09feb12b":http://emportal.nysbc.org/myamiweb/imageviewer.php?expId=6433 | 50S Ribosomesubunit, RCT data | |
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| 21 | h2. Download Raw Stacks |
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| 23 | bq. *Note:* all stacks have been CTF corrected using a Weiner filter with ACE2, a variation of the ACE1 algorithm described in "Mallick _el al._, 2005":http://www.ncbi.nlm.nih.gov/pubmed/15935913 |
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| 25 | table{border:1px solid black}. |
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| 26 | {background:#ddd}. |Name|IMAGIC .hed file|IMAGIC .img file| |
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| 27 | |Projection-matching refinement stack|"start.hed":http://emg.nysbc.org/experiment/data/stacks/sub1485/start.hed|"start.img":http://emg.nysbc.org/experiment/data/stacks/sub1485/start.img| |
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| 28 | |Common lines stack|"start.hed":http://emg.nysbc.org/experiment/data/stacks/stack4/start.hed|"start.img":http://emg.nysbc.org/experiment/data/stacks/stack4/start.img| |
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| 29 | |Untilted random conical tilt (RCT) stack|"start.hed":http://emg.nysbc.org/experiment/data/stacks/notstack3/start.hed|"start.img":http://emg.nysbc.org/experiment/data/stacks/notstack3/start.img| |
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| 30 | |Tilted random conical tilt (RCT) stack|"start.hed":http://emg.nysbc.org/experiment/data/stacks/tiltstack4/start.hed|"start.img":http://emg.nysbc.org/experiment/data/stacks/tiltstack4/start.img| |
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| 31 | |Synthetic 50S projections stack|"ctfstack_snr0.05.hed":http://emg.nysbc.org/experiment/data/stacks/syntheticData/dataset6/ctfstack_snr0.05.hed|"ctfstack_snr0.05.img":http://emg.nysbc.org/experiment/data/stacks/syntheticData/dataset6/ctfstack_snr0.05.img| |
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| 33 | h2. Download Tomography tilt series stack and tilts |
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| 35 | The tilt stack file is a 32-bit real mrc file without extended header. Combined with the information in the tilt angle (.rawtilt) file, it can be used in most tomography packages. |
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| 36 | |||
| 37 | table{border:1px solid black}. |
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| 38 | {background:#ddd}. |Name|rawtilt text file|tiltstack mrc file| |
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| 39 | |Tilt series 6|"09feb18c_006.rawtlt":http://emg.nysbc.org/experiment/data/stacks/tomotiltseries6/09feb18c_006.rawtlt|"09feb18c_006.st":http://emg.nysbc.org/experiment/data/stacks/tomotiltseries6/09feb18c_006.st| |
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| 41 | h2. Download initial models and final reconstructions |
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| 42 | |||
| 43 | bq. *Note:* Refinement was done using the EMAN1 refine program for 12 iterations. Final reconstruction are the raw volume from EMAN, no amplitude correction has been performed. |
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| 44 | |||
| 45 | table{border:1px solid black}. |
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| 46 | {background:#ddd}. |Name|Initial model|Final reconstruction| |
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| 47 | |\3{text-align:center}. _Ab initio_ models | |
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| 48 | | PDB structure | "download model":http://emg.nysbc.org/experiment/data/models/accepted/density57_09apr27q54/density057-1_55apix-20_0res-200box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/pdbrecon12/threed.12a.mrc | |
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| 49 | | EMDB structure | "download model":http://emg.nysbc.org/experiment/data/models/accepted/density61_09may06n36/density061-1_55apix-7_5res-200box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/emdbrecon10/threed.12a.mrc | |
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| 50 | | Angular reconstitution | "download model":http://emg.nysbc.org/experiment/data/models/accepted/file_09jul21k04/filt.mrc-1_95apix-15_0res-160box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/clrecon12/threed.12a.mrc | |
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| 51 | | Cross-common lines (improved class averages) | "download model":http://emg.nysbc.org/experiment/data/models/accepted/file_09aug04n04/filt.mrc-1_95apix-30_0res-140box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/emancl_goodavgs/threed.12a.mrc | |
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| 52 | | Random conical tilt (RCT) | "download model":http://emg.nysbc.org/experiment/data/models/accepted/09may06o12/rct.mrc-1_55apix-39_0res-216box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/rctrecon10/threed.12a.mrc | |
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| 53 | | Sub-tomogram averaging | "download model":http://emg.nysbc.org/experiment/data/models/accepted/09may06n58/tomo.mrc-6_18apix-30_0res-64box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/tomorecon7/threed.12a.mrc | |
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| 54 | |\3{text-align:center}. Poor models | |
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| 55 | | Hemisphere | "download model":http://emg.nysbc.org/experiment/data/models/accepted/09jul29l35/hemisphere-3_1apix-30_0res-128box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/hemirecon16/threed.12a.mrc | |
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| 56 | | Symmetric Gaussian sphere | "download model":http://emg.nysbc.org/experiment/data/models/accepted/09jul29l37/gauss_sphere.mrc-3_1apix-30_0res-128box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/ssrecon14/threed.12a.mrc | |
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| 57 | | Asymmetric Gaussian sphere | "download model":http://emg.nysbc.org/experiment/data/models/accepted/09jul29l36/gauss_sphere_asymm.mrc-3_1apix-30_0res-128box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/asrecon15/threed.12a.mrc | |
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| 58 | | Angular reconstitution (poor class averages) | "download model":http://emg.nysbc.org/experiment/data/models/accepted/file_09aug05v25/filt.mrc-3_1apix-30_0res-100box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/recon20/threed.12a.mrc | |
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| 59 | | Cross-common lines (poor class averages) | "download model":http://emg.nysbc.org/experiment/data/models/accepted/eman_startAny/threed-1_95apix-60_0res-160box.mrc | "download density":http://emg.nysbc.org/experiment/data/recon/emanclrecon18/threed.12a.mrc | |
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| 61 | h2. Reference |
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| 62 | |||
| 63 | Voss, Lyumkis, Cheng, _et al._ (2010) |
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| 64 | "_A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy._":http://www.ncbi.nlm.nih.gov/pubmed/20018246 |
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| 65 | J Struct Biol. v169(3): pp. 389-98. |