# Errata to “DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map”

Deng Luo, Zainab Alsuwaykit, Dawar Khan, Ondřej Strnad, Tobias Isenberg, Ivan Viola

► To cite this version:

Deng Luo, Zainab Alsuwaykit, Dawar Khan, Ondřej Strnad, Tobias Isenberg, et al.. Errata to “DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map”. IEEE Transactions on Visualization and Computer Graphics, 2025, 31 (2), pp.1645-1646. 10.1109/TVCG.2024.3502911. hal-04869601

HAL Id: hal-04869601

https://inria.hal.science/hal-04869601v1

Submitted on 7 Jan 2025

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<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
Errata to “DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map” by Deng Luo, Zainab Alsuwaykit, Dawar Khan, Ondřej Strnad, Tobias Isenberg, Ivan Viola (Digital Object Identifier no. 10.1109/TVCG.2024.3456404)

The authors would like to make the following errata after correcting the initialization related bugs in the associated program.

On page 1, the last two sentences of Fig. 1's caption should be "Right: the final composited structure overlaid on the original target volume (RMSD: 0.138). The involved computation takes 10 seconds in total, and the human-in-the-loop interaction takes ≈3 minutes." On page 5, "10-element array" should be "3-element array." On page 10, in the ACKNOWLEDGMENTS section, the authors add: "The authors also thank Alexandra Irger for her narration in the submission video." The authors also make changes to Fig. 3 (c–f), Fig. 4, Table 1–3, which are attached below, and an updated attachment "ExpRes.xlsx" in the supplementary materials.

<figure><img src="image_2.png" /><figcaption>Fig. 3: Clustering and filtering: (a) target volume, (b) atom coordinates of the source structure, (c) positions of 1000 fit results (the dots are clustered, hiding the number of results), (d) 1000 instances of the structure, (e) positions of 1000 fit results with a transparency level set based on an exponential scaling of the sum of sampled density metric (two clusters stand out, as in the zoom-in insets), and (f) instances of the structure at those two clusters.</figcaption></figure>
<figure><img src="image_3.png" /><figcaption>Fig. 4: Visual browser based on ChimeraX. The target volume on the middle is overlaid with a fitted molecule corresponding to the selected fit result in the table on the left (clustered fits, each row is the representative placement with the highest correlation from that cluster). After inspection, users can save the placement and then select “Simulate volume” and “Zero density” to zero out the corresponding voxels from the target volume.</figcaption></figure>
<table><caption>Table 1</caption><thead><tr><th rowspan="2">PDB</th><th rowspan="2">Res</th><th colspan="3">Hit rate</th><th colspan="3">Computing time</th><th colspan="4">RMSD (Å)</th></tr><tr><th>C</th><th>D</th><th>G</th><th>C</th><th>D</th><th>G</th><th>M</th><th>C</th><th>D</th><th>DC</th></tr></thead><tbody><tr><td>6WTI</td><td>2.38</td><td>0.0</td><td><strong>136.8</strong></td><td>n/a</td><td>150.3</td><td><strong>3.8</strong></td><td>39.7</td><td>1.310</td><td>n/a</td><td>0.942</td><td><strong>0.037</strong></td></tr><tr><td>7D8X</td><td>2.60</td><td>0.0</td><td><strong>202.0</strong></td><td>n/a</td><td>196.0</td><td><strong>5.2</strong></td><td>37.6</td><td>1.960</td><td>n/a</td><td>0.984</td><td><strong>0.014</strong></td></tr><tr><td>7SP8</td><td>2.70</td><td>4.6</td><td><strong>188</strong></td><td>40.9</td><td>130.6</td><td><strong>2.6</strong></td><td>50.5</td><td>1.290</td><td>0.996</td><td>0.969</td><td><strong>0.025</strong></td></tr><tr><td>7STE</td><td>2.73</td><td>14.0</td><td><strong>110.4</strong></td><td>7.9</td><td>806.1</td><td><strong>12.1</strong></td><td>66.6</td><td>1.740</td><td>0.062</td><td>0.662</td><td><strong>0.058</strong></td></tr><tr><td>7JPO</td><td>3.20</td><td>5.4</td><td><strong>191.8</strong></td><td>35.5</td><td>250.7</td><td><strong>6.7</strong></td><td>37.2</td><td>2.540</td><td>0.017</td><td>0.922</td><td><strong>0.015</strong></td></tr><tr><td>7PM0</td><td>3.60</td><td>44.0</td><td><strong>195.4</strong></td><td>4.4</td><td>352.4</td><td><strong>4.1</strong></td><td>86.7</td><td>1.640</td><td>0.030</td><td>0.907</td><td><strong>0.024</strong></td></tr><tr><td>6MSU</td><td>3.80</td><td>0.0</td><td><strong>105.0</strong></td><td>n/a</td><td>162.2</td><td><strong>4.1</strong></td><td>39.2</td><td>2.360</td><td>n/a</td><td>0.912</td><td><strong>0.018</strong></td></tr><tr><td>6ME0</td><td>3.90</td><td>7.4</td><td><strong>116.0</strong></td><td>15.7</td><td>128.2</td><td><strong>3.2</strong></td><td>40.1</td><td>1.940</td><td>0.489</td><td>0.786</td><td><strong>0.488</strong></td></tr><tr><td>7MGE</td><td>3.94</td><td>4.8</td><td><strong>123.6</strong></td><td>25.8</td><td>337.6</td><td><strong>4.3</strong></td><td>78.1</td><td>1.870</td><td><strong>0.017</strong></td><td>0.819</td><td><strong>0.017</strong></td></tr><tr><td>High-avg</td><td></td><td>8.9</td><td><strong>152.1</strong></td><td>21.7</td><td>279.3</td><td><strong>5.1</strong></td><td>52.8</td><td>1.850</td><td>0.268</td><td>0.878</td><td><strong>0.077</strong></td></tr><tr><td>5NL2</td><td>6.60</td><td>1.8</td><td><strong>163.2</strong></td><td>90.7</td><td>94.6</td><td><strong>2.0</strong></td><td>48.0</td><td>2.440</td><td>0.093</td><td>1.124</td><td><strong>0.056</strong></td></tr><tr><td>7K2V</td><td>6.60</td><td>49.0</td><td><strong>165.6</strong></td><td>3.4</td><td>240.6</td><td><strong>4.1</strong></td><td>58.2</td><td>25.290</td><td><strong>0.338</strong></td><td>1.323</td><td><strong>0.338</strong></td></tr><tr><td>7CA5</td><td>7.60</td><td>55.8</td><td><strong>72.4</strong></td><td>1.3</td><td>322.6</td><td><strong>2.9</strong></td><td>110.0</td><td>3.290</td><td>2.042</td><td><strong>1.207</strong></td><td>2.042</td></tr><tr><td>5VH9</td><td>7.70</td><td>68.6</td><td><strong>158.0</strong></td><td>2.3</td><td>1147.8</td><td><strong>14.1</strong></td><td>81.3</td><td>0.960</td><td><strong>0.085</strong></td><td>0.991</td><td><strong>0.085</strong></td></tr><tr><td>6AR6</td><td>9.00</td><td>78.0</td><td><strong>182.6</strong></td><td>2.3</td><td>74.9</td><td><strong>1.5</strong></td><td>49.3</td><td>2.200</td><td>0.123</td><td>2.617</td><td><strong>0.117</strong></td></tr><tr><td>3J1Z</td><td>13.00</td><td>138.6</td><td><strong>172.2</strong></td><td>1.2</td><td>64.4</td><td><strong>2.0</strong></td><td>33.0</td><td>32.330</td><td>0.396</td><td>2.612</td><td><strong>0.388</strong></td></tr><tr><td>Med-avg</td><td></td><td>65.3</td><td><strong>152.3</strong></td><td>16.9</td><td>324.1</td><td><strong>4.4</strong></td><td>63.3</td><td>11.085</td><td>0.513</td><td>1.646</td><td><strong>0.504</strong></td></tr><tr><td>All-avg</td><td></td><td>31.5</td><td><strong>152.2</strong></td><td>19.8</td><td>297.3</td><td><strong>4.9</strong></td><td>57.0</td><td>5.544</td><td>0.366</td><td>1.185</td><td><strong>0.248</strong></td></tr></tbody></table>

<table><caption>Table 2</caption><thead><tr><th>Structure</th><th>C Hit</th><th>D Hit</th><th>Gain</th></tr></thead><tbody><tr><td>17MLV6_D3</td><td>108</td><td>254</td><td>2.4x</td></tr><tr><td>17M317_D1</td><td>127</td><td>240</td><td>1.9x</td></tr></tbody></table>

<table><caption>Table 3</caption><thead><tr><th rowspan="2">PDB</th><th rowspan="2">EMDB</th><th rowspan="2">#S</th><th rowspan="2">#A</th><th rowspan="2">Res</th><th rowspan="2">Vs</th><th rowspan="2">L</th><th colspan="3">Hit rate</th><th colspan="3">Computing time</th><th colspan="4">RMSD (Å)</th></tr><tr><th>C</th><th>D</th><th>G</th><th>C</th><th>D</th><th>G</th><th>M</th><th>C</th><th>D</th><th>DC</th></tr></thead><tbody><tr><td>6WTI</td><td>21897</td><td>4</td><td>9,980</td><td>2.38</td><td>1.08</td><td>0.7660</td><td>0.0</td><td><strong>136.8</strong></td><td>n/a</td><td>150.3</td><td><strong>3.8</strong></td><td>39.7</td><td>1.310</td><td>n/a</td><td>0.942</td><td><strong>0.037</strong></td></tr><tr><td>7D8X</td><td>30614</td><td>4</td><td>10,928</td><td>2.60</td><td>1.08</td><td>0.0229</td><td>0.0</td><td><strong>202.0</strong></td><td>n/a</td><td>196.0</td><td><strong>5.2</strong></td><td>37.6</td><td>1.960</td><td>n/a</td><td>0.984</td><td><strong>0.014</strong></td></tr><tr><td>7SP8</td><td>25368</td><td>3</td><td>6,090</td><td>2.70</td><td>1.08</td><td>5.5755</td><td>4.6</td><td><strong>188</strong></td><td>40.9</td><td>130.6</td><td><strong>2.6</strong></td><td>50.5</td><td>1.290</td><td>0.996</td><td>0.969</td><td><strong>0.025</strong></td></tr><tr><td>7STE</td><td>25426</td><td>5</td><td>14,249</td><td>2.73</td><td>0.83</td><td>0.0963</td><td>14.0</td><td><strong>110.4</strong></td><td>7.9</td><td>806.1</td><td><strong>12.1</strong></td><td>66.6</td><td>1.740</td><td>0.062</td><td>0.662</td><td><strong>0.058</strong></td></tr><tr><td>7JPO</td><td>22417</td><td>5</td><td>16,087</td><td>3.20</td><td>1.07</td><td>0.0240</td><td>5.4</td><td><strong>191.8</strong></td><td>35.5</td><td>250.7</td><td><strong>6.7</strong></td><td>37.2</td><td>2.540</td><td>0.017</td><td>0.922</td><td><strong>0.015</strong></td></tr><tr><td>7PM0</td><td>13508</td><td>3</td><td>10,169</td><td>3.60</td><td>1.10</td><td>0.0068</td><td>44.0</td><td><strong>195.4</strong></td><td>4.4</td><td>352.4</td><td><strong>4.1</strong></td><td>86.7</td><td>1.640</td><td>0.030</td><td>0.907</td><td><strong>0.024</strong></td></tr><tr><td>6MSU</td><td>30093</td><td>3</td><td>10,549</td><td>3.80</td><td>1.06</td><td>0.0350</td><td>0.0</td><td><strong>105.0</strong></td><td>n/a</td><td>162.2</td><td><strong>4.1</strong></td><td>39.2</td><td>2.360</td><td>n/a</td><td>0.912</td><td><strong>0.018</strong></td></tr><tr><td>6ME0</td><td>9108</td><td>3</td><td>7,465</td><td>3.90</td><td>1.06</td><td>0.0500</td><td>7.4</td><td><strong>116.0</strong></td><td>15.7</td><td>128.2</td><td><strong>3.2</strong></td><td>40.1</td><td>1.940</td><td>0.489</td><td>0.786</td><td><strong>0.488</strong></td></tr><tr><td>7MGE</td><td>23827</td><td>4</td><td>9,010</td><td>3.94</td><td>0.94</td><td>0.2550</td><td>4.8</td><td><strong>123.6</strong></td><td>25.8</td><td>337.6</td><td><strong>4.3</strong></td><td>78.1</td><td>1.870</td><td><strong>0.017</strong></td><td>0.819</td><td><strong>0.017</strong></td></tr><tr><td>High-avg</td><td></td><td>3.78</td><td>10,503</td><td>3.21</td><td>1.03</td><td>n/a</td><td>8.9</td><td><strong>152.1</strong></td><td>21.7</td><td>279.3</td><td><strong>5.1</strong></td><td>52.8</td><td>1.850</td><td>0.268</td><td>0.878</td><td><strong>0.077</strong></td></tr><tr><td>5NL2</td><td>3658</td><td>2</td><td>4,312</td><td>6.60</td><td>1.35</td><td>0.0297</td><td>1.8</td><td><strong>163.2</strong></td><td>90.7</td><td>94.6</td><td><strong>2.0</strong></td><td>48.0</td><td>2.440</td><td>0.093</td><td>1.124</td><td><strong>0.056</strong></td></tr><tr><td>7K2V</td><td>22647</td><td>2</td><td>5,717</td><td>6.60</td><td>1.05</td><td>0.0050</td><td>49.0</td><td><strong>165.6</strong></td><td>3.4</td><td>240.6</td><td><strong>4.1</strong></td><td>58.2</td><td>25.290</td><td><strong>0.338</strong></td><td>1.323</td><td><strong>0.338</strong></td></tr><tr><td>7CA5</td><td>30324</td><td>2</td><td>6,484</td><td>7.60</td><td>1.06</td><td>0.0100</td><td>55.8</td><td><strong>72.4</strong></td><td>1.3</td><td>322.6</td><td><strong>2.9</strong></td><td>110.0</td><td>3.290</td><td>2.042</td><td><strong>1.207</strong></td><td>2.042</td></tr><tr><td>5VH9</td><td>8673</td><td>2</td><td>22,042</td><td>7.70</td><td>1.20</td><td>0.0074</td><td>68.6</td><td><strong>158.0</strong></td><td>2.3</td><td>1147.8</td><td><strong>14.1</strong></td><td>81.3</td><td>0.960</td><td><strong>0.085</strong></td><td>0.991</td><td><strong>0.085</strong></td></tr><tr><td>6AR6</td><td>8898</td><td>2</td><td>2,395</td><td>9.00</td><td>3.00</td><td>0.0739</td><td>78.0</td><td><strong>182.6</strong></td><td>2.3</td><td>74.9</td><td><strong>1.5</strong></td><td>49.3</td><td>2.200</td><td>0.123</td><td>2.617</td><td><strong>0.117</strong></td></tr><tr><td>3J1Z</td><td>5450</td><td>2</td><td>4,586</td><td>13.00</td><td>2.74</td><td>3.8989</td><td>138.6</td><td><strong>172.2</strong></td><td>1.2</td><td>64.4</td><td><strong>2.0</strong></td><td>33.0</td><td>32.330</td><td>0.396</td><td>2.612</td><td><strong>0.388</strong></td></tr><tr><td>Med-avg</td><td></td><td>2.00</td><td>7,589</td><td>8.42</td><td>1.73</td><td>n/a</td><td>65.3</td><td><strong>152.3</strong></td><td>16.9</td><td>324.1</td><td><strong>4.4</strong></td><td>63.3</td><td>11.085</td><td>0.513</td><td>1.646</td><td><strong>0.504</strong></td></tr><tr><td>All-avg</td><td></td><td>3.01</td><td>9,337</td><td>5.29</td><td>1.31</td><td>n/a</td><td>31.5</td><td><strong>152.2</strong></td><td>19.8</td><td>297.3</td><td><strong>4.9</strong></td><td>57.0</td><td>5.544</td><td>0.366</td><td>1.185</td><td><strong>0.248</strong></td></tr></tbody></table>