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<h1 id="sars-cov-2">SARS-Cov-2</h1>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image.png" /></p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-1.png" /></p>
<p>在本教程中,我们将制作 SARS-Cov-2 病毒的结构可视化。请确保您已阅读<a href="step_by_step.md">分步指南</a>以了解插件的基本使用方法,并确保插件版本为 v1.0.2 或更高!</p>
<p>研究数据来自 2020 年 9 月发表在 Cell Press 的论文(<a href="https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4">https://www.cell.com/cell/fulltext/S0092-8674(20)31159-4</a>),作者是清华大学李赛团队。该研究使用冷冻电子断层扫描(cryo-ET)和亚断层图平均(STA)揭示了真实 SARS-CoV-2 病毒的分子组装。以下是该研究的官方视频:</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/JSKl5VY4k5w?si=t4LhrCRebxrX_Saf&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
<p>"冠状病毒如何将约 30kb 的 RNA 包装到约 80nm 直径的病毒腔内仍然是个谜。RNP 彼此之间是否有序以避免 RNA 缠结、打结或损坏,还是它们参与病毒组装?" 论文中提出了三类组装方式,我们将基于真实的冷冻电镜数据,制作"巢中蛋"形 RNP 组装的可视化。</p>
<h2 id="_1">下载和导入数据</h2>
<p>该研究的数据托管在 EMDB(<a href="https://www.ebi.ac.uk/emdb">https://www.ebi.ac.uk/emdb</a>),SARS-Cov-2 病毒网站是<a href="https://www.ebi.ac.uk/emdb/EMD-30430">这里</a>。打开页面,找到"Download"按钮,选择第一个选项"3D Volume (.map.gz)"。</p>
<p>如果您无法下载数据,可以从这里下载。</p>
<p><a href="https://drive.google.com/file/d/1LMybsmTVbwQ38_eqAx6hbZTc5p2fdcjK/view?usp=sharing">SARS-Cov-2.map</a></p>
<p>下载后,放到任意目录并导入数据。在导入选项中,建议将 Bioxel Size 调整为 5,以减小数据形状,提高计算和渲染速度。如果您对硬件性能有信心,可以保持原始的 2.72 不变。调整 Bioxel Size 后,下方会根据当前的 bioxel size 计算转换后数据的形状。数据量会随着形状增大呈指数增长,可能会导致内存不足(OOM)。</p>
<h2 id="_2">切割病毒</h2>
<p>导入后,您可以通过创建和连接节点并设置参数来获取病毒,如下图所示。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-2.png" /></p>
<p>按下图所示放置灯光和相机。背光是区域光,白色,强度 500W,扩散 90°;在病毒内部放置一个点光源,颜色 <code>FFD08D</code>,强度 5W。相机焦距为 200mm。背景颜色为纯黑色。颜色管理的 Look 为 High Contrast。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-3.png" /></p>
<p>继续编辑节点,接着是"Set Properties"和"Set Color by Ramp 4"节点,这两个节点的参数设置如下图,其中颜色部分,从上到下设置为 <code>E1D0FC</code>(1.0)、<code>FFE42D</code>(0.5)、<code>3793FF</code>(0.5)、<code>FFFF8EC</code>(0.1)(括号中为 alpha 值)。颜色的 alpha 值也会影响密度。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-4.png" /></p>
<p>如果您觉得渲染太慢,请参阅<a href="improve_performance.md">这里</a>获取建议。</p>
<h2 id="rnp">单独为 RNP 着色</h2>
<p>当前的渲染效果很好,但考虑到我的目标是让您清楚看到 RNP 在病毒内部的排列方式,RNP 应该与其他部分用不同颜色着色。那么如何单独为 RNP 着色呢?</p>
<p>首先,我们必须分离 RNP。RNP 的值介于膜和 S 蛋白之间,因此很难分离。好在病毒是球形的,我们可以使用球形切割器将病毒的 RNP 部分与其余部分分离。为此,在容器的几何节点面板菜单中,点击 <strong>Bioxel Nodes &gt; Add a Cutter &gt; Sphere Cutter</strong>,并适当调整新创建的名为"Sphere_Cutter"的球体对象的大小和位置,使其恰好能将病毒内部的 RNP 和膜分离。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-5.png" /></p>
<p>改变"Sphere_Cutter"对象的位置可能会非常卡顿,此时您可以关闭"With Surface"并在 Slice Viewer 模式下操作。满意后,恢复设置。</p>
<p>然后在"Sphere Cutter"节点中打开 Invert,您可以看到相反的结果。这样我们就成功将两者分离了。接下来让我们分别着色,最后用 Join Component 合并。按如下图所示创建和连接节点,其中第二个 Cutter 节点是复制的,Set Color 中的颜色值设置为 <code>FFDDFE</code>(0.5)。如果一切正常,渲染结果应该如下图所示。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-6.png" /></p>
<p>此时,SARS-Cov-2 病毒的渲染完成了!</p>
<h2 id="rnp_1">渲染 RNP 和膜</h2>
<p>写实渲染很棒,但非写实渲染(NPR)在呈现结构信息方面更好。因此,我将使用卡通着色器来渲染 RNP 组装的首尾结构。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-7.png" /></p>
<p>RNP 的轮廓使用 Blender 的线稿(Line Art)功能,但线稿必须基于网格。选择挤出 RNP 的节点(即负责切割出 RNP 的"Cut"节点),右键点击 <strong>Bioxel Nodes &gt; Extract Mesh</strong>。这将为您创建一个 RNP 的新网格对象。</p>
<p>用同样的方式提取膜网格。</p>
<p>膜的病毒值远高于其他部分,因此让我们创建一个新的"Cutout"节点,同样在 ReCenter 之后,但阈值调整为 0.13。Cutout 后,连接到"To Surface"节点并按如下图所示设置参数,注意 Remove Island Threshold 设置为 1000,以便消除小于 1000 pts 的任何碎片。然后选择"To Surface"节点,执行提取网格的操作。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-8.png" /></p>
<p>膜的网格需要切成两半,这可以通过雕刻模式中的 Box Trim 笔刷或布尔修改器来完成。RNP 的网格也可能需要一些修复工作,我清理了一些 RNP 的破损表面。所有网格现在都可以使用了。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-9.png" /></p>
<p>关于线稿,请参阅 Blender Secrets 的视频教程。</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/aIWdBq7-ias?si=CrcStx5VVJBwDpzu&amp;controls=0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
<p>最后,RNP 超微结构的信息图完成了!</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-1.png" /></p>
<p>如果您按照文档有困难,可以下载项目文件。</p>
<p><a href="https://drive.google.com/file/d/15GpIoIjVAE-Jr98zWo7oupuk1KfRVPmk/view?usp=sharing">SARS-Cov-2.zip</a></p>
<h2 id="_3">作业</h2>
<p>论文中提供了其他相关数据,您可以尝试可视化它们。</p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-10.png" /></p>
<p>前往官方 EMDB 网站 https://www.ebi.ac.uk/emdb/,在搜索框中输入 EMD 编号即可获取。</p>
<p>电子显微镜数据银行(EMDB)是一个公共仓库,用于存放冷冻样品的电子显微镜(cryoEM)体积和代表性断层图。如果您想获取其他病毒的数据,只需在搜索框中输入其名称即可。例如,乙型肝炎病毒,在搜索框中输入,然后选择左侧 Sample Type 中的 Virus,下载您需要的数据(最好找到相应的论文来明确数据信息)。</p>
<p><strong>尝试可视化乙型肝炎病毒。</strong></p>
<p><img alt="alt text" src="../assets/SARS-Cov-2/image-11.png" /></p>
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