DAQ-Score

Job ID : e733a936990c11b60e0d3d25b015f845

DAQ is a computational tool employing deep learning to estimate residue-wise local quality for protein models derived from cryo-EM maps (target resolution: 0-5 A). It generates a file in .pdb format documenting the scored structure, with scores stored in the B-factor column

Our result webpage comprises three tabs: Results Visualization, Output Logs, and Job Configuration.

The 'Result Visualization' panel showcases the protein structure scored by DAQ-Score, with the DAQ(AA) score stored in the b-factor column.
The 3D model is color-coded based on the DAQ(AA) score, ranging from red (-1.0) to blue (1.0). Blue represents a good score, while red signifies a lower score from DAQ.
On the right-hand side, you'll find the 'Download Outputs' button to acquire the modeled structure in .pdb format. You can utilize 'spectrum b, red_white_blue, all, -1,1' in PyMol to visualize the score.
Additionally, you can visualize the map online by clicking the "Show map" button. Once loaded, the default contour level matches your input; however, you can make adjustments by clicking the "..." button beside "isosurface." Within the "Type: Isosurface" option, you can modify the iso-surface value and opacity by scrolling through the bar for precise adjustments. This feature allows you to assess the alignment between the modeled structure and the map.

Output Logs:
The 'Output Logs' panel compiles all outputs generated by the scripts.
If you're interested in monitoring the job's progress during execution, this section provides a comprehensive overview.

Job Configuration:
In the 'Job Configuration' panel, you'll find the input parameters used for this specific job. These records serve to maintain a log of your submitted input for reference.

Problem Debugging:
For any troubleshooting needs: Should you encounter any issues, please don't hesitate to contact us via email to report the problems. When sending an email, kindly use the subject line format 'DAQ-score problem: [jobid]', where [jobid] corresponds to the job displayed in the title. This specific identification helps us efficiently locate and debug jobs in the backend, ensuring a prompt response to your concerns.

Contact:
dkihara@purdue.edu, gterashi@purdue.edu, xiaowang20140001@gmail.com.

DAQ is a computational tool using deep learning that can estimate the residue-wise local quality for protein models from cryo-Electron Microscopy (EM) maps.
The 3D model is colored by DAQ(AA) score scaled from red (-1.0) to blue (1.0) with a 19 residues sliding window. Here blue indicates good score, while red indicates bad score from DAQ.
If you encounter any questions for the scored structure, feel free to email dkihara@purdue.edu, gterashi@purdue.edu and wang3702@purdue.edu.

DAQ Started
gcc -O3 -c chkcmdline.c
gcc -O3 -c mrc.c -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
gcc -O3 -c readpdb.c -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
gcc -o TrimMapAtom main.c chkcmdline.o mrc.o readpdb.o -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
gcc -std=c99 -o DAQscore_colab main.c chkcmdline.o mrc.o readpdb.o thread.o dp.o -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
/bio/kihara-web/www/em/em-web-server/media/jobs/output/e733a936990c11b60e0d3d25b015f845/ existed
Origin: (356.44003, 155.44, 159.46)
Previous voxel size: 1.340000033378601
Previouse size: (35, 52, 47) Current map size: 46 69 62
Finished resizing 10/46
Finished resizing 20/46
Finished resizing 30/46
Finished resizing 40/46
nx : 35
ny : 52
nz : 47
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 35
my : 52
mz : 47
cella : (46.9, 69.68, 62.980003)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -0.3863585889339447
dmax : 0.8640021085739136
dmean : 0.014420190826058388
ispg : 0
nsymbt : 0
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map : b'MAP '
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cella : (46., 69., 62.)
cellb : (90., 90., 90.)
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dmin : -0.2989257276058197
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dmean : 0.015050053596496582
ispg : 1
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map : b'MAP '
machst : [68 68 0 0]
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nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 17:19:54 '
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----------------------------------------------------------------------------------------------------
resizing finished!
----------------------------------------------------------------------------------------------------
Finished processing model input!
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Our predictions are saved in /bio/kihara-web/www/em/em-web-server/media/jobs/output/e733a936990c11b60e0d3d25b015f845/prediction.txt, please have a check!
total different chains: {'9'}
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[['9', ' N ', 372.071, 168.995, 189.063], ['9', ' CA ', 373.156, 169.833, 188.552], ['9', ' C ', 374.09, 170.232, 189.69], ['9', ' O ', 375.32, 170.151, 189.567], ['9', ' CB ', 372.599, 171.08, 187.853], ['9', ' CG ', 373.651, 172.079, 187.445], ['9', ' CD1', 374.075, 173.066, 188.331], ['9', ' CD2', 374.206, 172.045, 186.173], ['9', ' CE1', 375.037, 173.99, 187.959], ['9', ' CE2', 375.168, 172.967, 185.796], ['9', ' CZ ', 375.584, 173.941, 186.689], ['9', ' H ', 371.152, 169.372, 188.879], ['9', ' HA ', 373.676, 169.322, 187.897], ['9', ' HB2', 372.128, 170.802, 187.052], ['9', ' HB3', 371.987, 171.532, 188.451], ['9', ' HD1', 373.71, 173.103, 189.185], ['9', ' HD2', 373.931, 171.393, 185.569], ['9', ' HE1', 375.314, 174.642, 188.561], ['9', ' HE2', 375.536, 172.932, 184.943], ['9', ' HZ ', 376.23, 174.56, 186.437]]
[['9', ' N ', 373.474, 170.659, 190.787], ['9', ' CA ', 374.195, 171.093, 191.986], ['9', ' C ', 375.065, 169.957, 192.507], ['9', ' O ', 376.236, 170.163, 192.84], ['9', ' CB ', 373.248, 171.597, 193.104], ['9', ' CG1', 372.568, 172.914, 192.697], ['9', ' CG2', 374.001, 171.781, 194.419], ['9', ' CD1', 373.469, 174.133, 192.692], ['9', ' H ', 372.47, 170.717, 190.879], ['9', ' HA ', 374.793, 171.829, 191.74], ['9', ' HB ', 372.557, 170.932, 193.244], ['9', 'HG12', 372.211, 172.824, 191.803], ['9', 'HG13', 371.848, 173.09, 193.32], ['9', 'HG21', 374.085, 170.931, 194.859], ['9', 'HG22', 373.505, 172.383, 194.979], ['9', 'HG23', 374.87, 172.148, 194.239], ['9', 'HD11', 373.771, 174.307, 193.585], ['9', 'HD12', 372.968, 174.885, 192.368], ['9', 'HD13', 374.22, 173.972, 192.117]]
[['9', ' N ', 374.463, 168.773, 192.565], ['9', ' CA ', 375.144, 167.566, 193.038], ['9', ' C ', 376.368, 167.283, 192.176], ['9', ' O ', 377.453, 166.992, 192.698], ['9', ' CB ', 374.197, 166.36, 193.098], ['9', ' CG ', 373.705, 166.029, 194.504], ['9', ' CD ', 373.37, 167.258, 195.336], ['9', ' NE2', 372.487, 168.105, 194.821], ['9', ' OE1', 373.907, 167.443, 196.428], ['9', ' H ', 373.501, 168.623, 192.297], ['9', ' HA ', 375.479, 167.736, 193.943], ['9', ' HB2', 373.419, 166.528, 192.545], ['9', ' HB3', 374.665, 165.577, 192.766], ['9', ' HG2', 372.901, 165.489, 194.434], ['9', ' HG3', 374.396, 165.532, 194.969], ['9', 'HE21', 372.423, 168.903, 195.136], ['9', 'HE22', 371.978, 167.857, 194.174]]
[['9', ' N ', 376.165, 167.384, 190.867], ['9', ' CA ', 377.225, 167.164, 189.881], ['9', ' C ', 378.383, 168.119, 190.127], ['9', ' O ', 379.557, 167.72, 190.136], ['9', ' H ', 375.275, 167.611, 190.447], ['9', ' HA2', 377.548, 166.251, 189.936], ['9', ' HA3', 376.872, 167.323, 188.995]]
[['9', ' N ', 378.019, 169.381, 190.332], ['9', ' CA ', 378.985, 170.453, 190.592], ['9', ' C ', 379.805, 170.132, 191.842], ['9', ' O ', 381.033, 170.254, 191.847], ['9', ' CB ', 378.284, 171.808, 190.749], ['9', ' OG ', 379.203, 172.821, 191.121], ['9', ' H ', 377.061, 169.701, 190.318], ['9', ' HA ', 379.602, 170.518, 189.834], ['9', ' HB2', 377.876, 172.049, 189.902], ['9', ' HB3', 377.603, 171.738, 191.434], ['9', ' HG ', 378.782, 173.554, 191.262]]
[['9', ' N ', 379.095, 169.73, 192.902], ['9', ' CA ', 379.666, 169.508, 194.241], ['9', ' C ', 380.146, 168.064, 194.461], ['9', ' O ', 379.915, 167.481, 195.523], ['9', ' CB ', 378.628, 169.869, 195.319], ['9', ' CG ', 378.404, 171.337, 195.691], ['9', ' CD1', 378.148, 172.239, 194.49], ['9', ' CD2', 377.247, 171.425, 196.678], ['9', ' H ', 378.103, 169.547, 192.862], ['9', ' HA ', 380.437, 170.101, 194.364], ['9', ' HB2', 377.769, 169.516, 195.041], ['9', ' HB3', 378.886, 169.435, 196.147], ['9', ' HG ', 379.198, 171.667, 196.141], ['9', 'HD11', 378.835, 172.108, 193.835], ['9', 'HD12', 378.155, 173.152, 194.785], ['9', 'HD13', 377.291, 172.028, 194.117], ['9', 'HD21', 376.449, 171.104, 196.252], ['9', 'HD22', 377.132, 172.34, 196.943], ['9', 'HD23', 377.45, 170.884, 197.445]]
[['9', ' N ', 380.819, 167.495, 193.464], ['9', ' CA ', 381.36, 166.144, 193.572], ['9', ' C ', 382.683, 166.176, 194.335], ['9', ' O ', 383.57, 166.968, 194.01], ['9', ' CB ', 381.575, 165.544, 192.18], ['9', ' H ', 381.016, 167.935, 192.578], ['9', ' HA ', 380.728, 165.57, 194.053], ['9', ' HB2', 380.726, 165.521, 191.712], ['9', ' HB3', 382.128, 166.13, 191.648]]
[['9', ' N ', 382.81, 165.318, 195.347], ['9', ' CA ', 384.065, 165.174, 196.093], ['9', ' C ', 385.178, 164.61, 195.204], ['9', ' O ', 386.36, 164.824, 195.476], ['9', ' CB ', 383.871, 164.274, 197.317], ['9', ' H ', 382.069, 164.712, 195.674], ['9', ' HA ', 384.35, 166.056, 196.41], ['9', ' HB2', 383.177, 164.652, 197.879], ['9', ' HB3', 383.493, 163.44, 197.05]]
[['9', ' N ', 384.789, 163.885, 194.153], ['9', ' CA ', 385.726, 163.405, 193.136], ['9', ' C ', 386.327, 164.557, 192.322], ['9', ' O ', 387.527, 164.559, 192.041], ['9', ' CB ', 385.031, 162.415, 192.196], ['9', ' H ', 383.836, 163.599, 193.981], ['9', ' HA ', 386.462, 162.932, 193.578], ['9', ' HB2', 384.708, 161.661, 192.714], ['9', ' HB3', 384.21, 162.785, 191.813]]
[['9', ' N ', 385.492, 165.527, 191.948], ['9', ' CA ', 385.943, 166.697, 191.187], ['9', ' C ', 386.687, 167.694, 192.078], ['9', ' O ', 387.534, 168.456, 191.608], ['9', ' CB ', 384.752, 167.39, 190.521], ['9', ' H ', 384.503, 165.531, 192.151], ['9', ' HA ', 386.555, 166.407, 190.479], ['9', ' HB2', 384.271, 166.742, 189.982], ['9', ' HB3', 384.037, 167.58, 191.157]]
[['9', ' N ', 383.868, 172.727, 193.773], ['9', ' CA ', 382.863, 173.472, 194.526], ['9', ' C ', 383.017, 173.232, 196.024], ['9', ' O ', 383.16, 174.178, 196.8], ['9', ' CB ', 381.457, 173.072, 194.074], ['9', ' H ', 384.677, 172.45, 194.312], ['9', ' HA ', 382.978, 174.43, 194.356], ['9', ' HB2', 381.342, 173.32, 193.144], ['9', ' HB3', 381.274, 172.127, 194.233]]
[['9', ' N ', 382.978, 171.96, 196.418], ['9', ' CA ', 383.217, 171.556, 197.806], ['9', ' C ', 384.71, 171.332, 198.07], ['9', ' O ', 385.176, 171.531, 199.191], ['9', ' CB ', 382.42, 170.294, 198.151], ['9', ' OG ', 382.742, 169.225, 197.279], ['9', ' H ', 382.785, 171.186, 195.798], ['9', ' HA ', 382.911, 172.266, 198.409], ['9', ' HB2', 382.627, 170.03, 199.061], ['9', ' HB3', 381.473, 170.489, 198.072], ['9', ' HG ', 382.243, 168.558, 197.438]]
[['9', ' N ', 385.451, 170.916, 197.04], ['9', ' CA ', 386.915, 170.815, 197.114], ['9', ' C ', 387.55, 172.198, 197.287], ['9', ' O ', 388.569, 172.345, 197.964], ['9', ' CB ', 387.474, 170.137, 195.858], ['9', ' H ', 385.074, 170.635, 196.146], ['9', ' HA ', 387.161, 170.267, 197.889], ['9', ' HB2', 387.055, 169.268, 195.755], ['9', ' HB3', 387.16, 170.638, 195.054]]
[['9', ' N ', 386.932, 173.202, 196.667], ['9', ' CA ', 387.317, 174.6, 196.83], ['9', ' C ', 386.952, 175.095, 198.222], ['9', ' O ', 387.723, 175.843, 198.83], ['9', ' CB ', 386.627, 175.505, 195.781], ['9', ' CG1', 387.067, 176.956, 195.948], ['9', ' CG2', 386.918, 175.015, 194.366], ['9', ' H ', 386.145, 173.07, 196.05], ['9', ' HA ', 388.286, 174.684, 196.717], ['9', ' HB ', 385.657, 175.468, 195.918], ['9', 'HG11', 386.554, 177.363, 196.651], ['9', 'HG12', 386.917, 177.429, 195.126], ['9', 'HG13', 388.0, 176.978, 196.17], ['9', 'HG21', 387.853, 174.81, 194.293], ['9', 'HG22', 386.684, 175.702, 193.737], ['9', 'HG23', 386.397, 174.229, 194.189]]
[['9', ' N ', 385.775, 174.683, 198.699], ['9', ' CA ', 385.277, 175.058, 200.017], ['9', ' C ', 386.256, 174.627, 201.093], ['9', ' O ', 386.568, 175.411, 202.001], ['9', ' CB ', 383.907, 174.43, 200.275], ['9', ' H ', 385.134, 174.098, 198.183], ['9', ' HA ', 385.181, 176.032, 200.061], ['9', ' HB2', 383.286, 174.735, 199.595], ['9', ' HB3', 383.98, 173.439, 200.221]]
[['9', ' N ', 386.73, 173.388, 200.966], ['9', ' CA ', 387.683, 172.81, 201.92], ['9', ' C ', 388.95, 173.659, 201.966], ['9', ' O ', 389.461, 173.976, 203.05], ['9', ' CB ', 388.041, 171.344, 201.575], ['9', ' CG1', 386.825, 170.432, 201.771], ['9', ' CG2', 389.19, 170.845, 202.446], ['9', ' CD1', 386.906, 169.123, 201.014], ['9', ' H ', 386.477, 172.763, 200.215], ['9', ' HA ', 387.281, 172.819, 202.814], ['9', ' HB ', 388.315, 171.301, 200.646], ['9', 'HG12', 386.741, 170.221, 202.714], ['9', 'HG13', 386.031, 170.892, 201.47], ['9', 'HG21', 390.023, 171.145, 202.074], ['9', 'HG22', 389.179, 169.886, 202.47], ['9', 'HG23', 389.084, 171.19, 203.336], ['9', 'HD11', 387.115, 169.307, 200.095], ['9', 'HD12', 386.058, 168.677, 201.073], ['9', 'HD13', 387.592, 168.575, 201.403]]
[['9', ' N ', 389.427, 174.013, 200.777], ['9', ' CA ', 390.634, 174.83, 200.619], ['9', ' C ', 390.457, 176.166, 201.332], ['9', ' O ', 391.35, 176.62, 202.063], ['9', ' CB ', 390.957, 175.045, 199.147], ['9', ' H ', 389.005, 173.746, 199.899], ['9', ' HA ', 391.391, 174.364, 201.031], ['9', ' HB1', 390.969, 174.195, 198.701], ['9', ' HB2', 391.818, 175.464, 199.076], ['9', ' HB3', 390.288, 175.611, 198.756]]
[['9', ' N ', 389.293, 176.767, 201.102], ['9', ' CA ', 388.933, 178.054, 201.698], ['9', ' C ', 388.982, 177.961, 203.218], ['9', ' O ', 389.541, 178.834, 203.896], ['9', ' CB ', 387.541, 178.492, 201.239], ['9', ' H ', 388.575, 176.391, 200.5], ['9', ' HA ', 389.579, 178.734, 201.411], ['9', ' HB2', 387.527, 178.537, 200.27], ['9', ' HB3', 386.878, 177.807, 201.495]]
[['9', ' N ', 388.387, 176.885, 203.725], ['9', ' CA ', 388.326, 176.609, 205.162], ['9', ' C ', 389.732, 176.529, 205.738], ['9', ' O ', 390.025, 177.119, 206.787], ['9', ' CB ', 387.577, 175.302, 205.429], ['9', ' H ', 387.928, 176.181, 203.164], ['9', ' HA ', 387.848, 177.336, 205.612], ['9', ' HB2', 386.682, 175.369, 205.059], ['9', ' HB3', 388.033, 174.556, 204.955]]
[['9', ' N ', 390.582, 175.793, 205.028], ['9', ' CA ', 391.98, 175.595, 205.413], ['9', ' C ', 392.689, 176.94, 205.518], ['9', ' O ', 393.407, 177.209, 206.494], ['9', ' CB ', 392.698, 174.701, 204.399], ['9', ' H ', 390.331, 175.309, 204.177], ['9', ' HA ', 392.016, 175.158, 206.289], ['9', ' HB2', 392.258, 173.837, 204.372], ['9', ' HB3', 392.663, 175.118, 203.5]]
[['9', ' N ', 392.465, 177.763, 204.497], ['9', ' CA ', 393.053, 179.101, 204.41], ['9', ' C ', 392.646, 179.931, 205.623], ['9', ' O ', 393.481, 180.596, 206.253], ['9', ' CB ', 392.61, 179.837, 203.131], ['9', ' H ', 391.883, 177.531, 203.705], ['9', ' HA ', 394.03, 179.026, 204.401], ['9', ' HB ', 391.618, 179.935, 203.124]]
[['9', ' N ', 391.352, 179.868, 205.925], ['9', ' CA ', 390.763, 180.595, 207.051], ['9', ' C ', 391.441, 180.18, 208.352], ['9', ' O ', 391.81, 181.026, 209.178], ['9', ' CB ', 389.261, 180.357, 207.128], ['9', ' H ', 390.679, 179.324, 205.403], ['9', ' HA ', 390.912, 181.555, 206.925], ['9', ' HB1', 388.871, 180.53, 206.267], ['9', ' HB2', 388.886, 180.952, 207.781], ['9', ' HB3', 389.098, 179.447, 207.385]]
[['9', ' N ', 391.593, 178.867, 208.502], ['9', ' CA ', 392.222, 178.269, 209.682], ['9', ' C ', 393.64, 178.803, 209.846], ['9', ' O ', 394.051, 179.19, 210.949], ['9', ' CB ', 392.245, 176.742, 209.57], ['9', ' H ', 391.284, 178.184, 207.825], ['9', ' HA ', 391.708, 178.511, 210.48], ['9', ' HB2', 391.334, 176.417, 209.494], ['9', ' HB3', 392.744, 176.48, 208.755]]
[['9', ' N ', 394.359, 178.814, 208.727], ['9', ' CA ', 395.738, 179.299, 208.676], ['9', ' C ', 395.816, 180.75, 209.155], ['9', ' O ', 396.682, 181.094, 209.97], ['9', ' CB ', 396.309, 179.165, 207.27], ['9', ' H ', 394.015, 178.487, 207.835], ['9', ' HA ', 396.288, 178.754, 209.277], ['9', ' HB1', 396.158, 178.271, 206.953], ['9', ' HB2', 397.252, 179.345, 207.301], ['9', ' HB3', 395.877, 179.796, 206.692]]
[['9', ' N ', 394.93, 181.603, 208.643], ['9', ' CA ', 394.915, 183.021, 209.012], ['9', ' C ', 394.212, 183.231, 210.349], ['9', ' O ', 394.761, 182.92, 211.406], ['9', ' CB ', 394.225, 183.851, 207.927], ['9', ' H ', 394.217, 181.347, 207.974], ['9', ' HA ', 395.835, 183.348, 209.097], ['9', ' HB2', 394.676, 183.703, 207.081], ['9', ' HB3', 393.308, 183.518, 207.751]]
Please check result here: /bio/kihara-web/www/em/em-web-server/media/jobs/output/e733a936990c11b60e0d3d25b015f845/daq_score_w9.pdb
Please open it in pymol and visualize it by putting the following command to Pymol:
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spectrum b, red_white_blue, all, -1,1
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INFO : DAQ Done









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