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diff --git a/2022/02/17/PaperRead-Day7/index.html b/2022/02/17/PaperRead-Day7/index.html
@@ -818,7 +818,7 @@ <h1 id="nascent-转录组测序揭示的-lncRNA-合成机制"><a href="#nascent-
                 <a href="/2022/02/17/RDataVisualization-other-unusual/">
                     <div class="card-image">
 
-                        <img src="https://liangshaw.github.io/2022/02/17/RDataVisualization-3/pymid-background.png" class="responsive-img" alt="R 常用绘图方法一. (金字塔图|镜面图|可视化合集)">
+                        <img src="/pymid-background.png" class="responsive-img" alt="R 常用绘图方法一. (金字塔图|镜面图|可视化合集)">
 
                         <span class="card-title">R 常用绘图方法一. (金字塔图|镜面图|可视化合集)</span>
                     </div>

diff --git a/2022/02/17/RDataVisualization-other-unusual/index.html b/2022/02/17/RDataVisualization-other-unusual/index.html
@@ -259,7 +259,7 @@
 
 
 
-<div class="bg-cover pd-header post-cover" style="background-image: url('https://liangshaw.github.io/2022/02/17/RDataVisualization-3/pymid-background.png')">
+<div class="bg-cover pd-header post-cover" style="background-image: url('/pymid-background.png')">
     <div class="container" style="right: 0px;left: 0px;">
         <div class="row">
             <div class="col s12 m12 l12">
@@ -416,7 +416,7 @@ <h1 class="description center-align post-title">R 常用绘图方法一. (金字
 
                 <div class="post-date info-break-policy">
                     <i class="far fa-calendar-check fa-fw"></i>更新日期:&nbsp;&nbsp;
-                    2023-01-12
+                    2024-03-13
                 </div>
 
 
@@ -605,7 +605,7 @@ <h1 id="用-circlize-包画圈圈图看各染色体上差异基因"><a href="#
 <img src="https://jokergoo.github.io/circlize_examples/example/otu.jpg" width="800">
 
 <p>官方 manual:<br><a target="_blank" rel="noopener" href="https://jokergoo.github.io/circlize/">circlize: circular visualization in R</a></p>
-<h1 id="背景图片来源"><a href="#背景图片来源" class="headerlink" title="背景图片来源"></a>背景图片来源</h1><p><a target="_blank" rel="noopener" href="https://www.nature.com/articles/s41591-022-02113-6/figures/2">Nat Med (2023): Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome</a></p>
+<h1 id="桑基图-Sankey"><a href="#桑基图-Sankey" class="headerlink" title="桑基图 (Sankey)"></a>桑基图 (Sankey)</h1><h1 id="背景图片来源"><a href="#背景图片来源" class="headerlink" title="背景图片来源"></a>背景图片来源</h1><p><a target="_blank" rel="noopener" href="https://www.nature.com/articles/s41591-022-02113-6/figures/2">Nat Med (2023): Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome</a></p>
 
 
             </div>

diff --git a/2022/02/18/PaperRead-Day8/index.html b/2022/02/18/PaperRead-Day8/index.html
@@ -870,7 +870,7 @@ <h1 id="CECR2-通过促进-NF-κB-信号通路和巨噬细胞介导的免疫抑
                 <a href="/2022/02/17/RDataVisualization-other-unusual/">
                     <div class="card-image">
 
-                        <img src="https://liangshaw.github.io/2022/02/17/RDataVisualization-3/pymid-background.png" class="responsive-img" alt="R 常用绘图方法一. (金字塔图|镜面图|可视化合集)">
+                        <img src="/pymid-background.png" class="responsive-img" alt="R 常用绘图方法一. (金字塔图|镜面图|可视化合集)">
 
                         <span class="card-title">R 常用绘图方法一. (金字塔图|镜面图|可视化合集)</span>
                     </div>

diff --git a/2023/02/10/RdataScience-data-reshape/index.html b/2023/02/10/RdataScience-data-reshape/index.html
@@ -5,7 +5,14 @@
 <head>
     <meta charset="utf-8">
     <meta name="keywords" content="R 数据科学：数据加工与重塑, Shaw">
-    <meta name="description" content="tidyverse">
+    <meta name="description" content="tidyversedplyr
+用 0 替换 NA
+## all NA
+df &amp;lt;- df %&amp;gt;% replace(is. na (.), 0)
+
+## 针对某一列
+df &amp;lt;- df %&amp;gt;% 
+  mutate(rebs">
     <meta http-equiv="X-UA-Compatible" content="IE=edge">
     <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=no">
     <meta name="renderer" content="webkit|ie-stand|ie-comp">
@@ -401,7 +408,7 @@ <h1 class="description center-align post-title">R 数据科学：数据加工与
 
                 <div class="post-date info-break-policy">
                     <i class="far fa-calendar-check fa-fw"></i>更新日期:&nbsp;&nbsp;
-                    2023-02-17
+                    2024-03-13
                 </div>
 
 
@@ -423,7 +430,28 @@ <h1 class="description center-align post-title">R 数据科学：数据加工与
 
         <div class="card-content article-card-content">
             <div id="articleContent">
-                <h1 id="tidyverse"><a href="#tidyverse" class="headerlink" title="tidyverse"></a>tidyverse</h1><h1 id=""><a href="#" class="headerlink" title=""></a></h1>
+                <h1 id="tidyverse"><a href="#tidyverse" class="headerlink" title="tidyverse"></a>tidyverse</h1><h1 id="dplyr"><a href="#dplyr" class="headerlink" title="dplyr"></a>dplyr</h1><ul>
+<li><p>用 0 替换 NA</p>
+<pre class="line-numbers language-R" data-language="R"><code class="language-R">## all NA
+df &lt;- df %&gt;% replace(is. na (.), 0)
+
+## 针对某一列
+df &lt;- df %&gt;% 
+  mutate(rebs = ifelse(is. na (rebs), 0, rebs), 
+         pts = ifelse(is. na (pts), 0, pts))<span aria-hidden="true" class="line-numbers-rows"><span></span><span></span><span></span><span></span><span></span><span></span><span></span></span></code></pre></li>
+<li><p>删除全是 NA 的行</p>
+<pre class="line-numbers language-R" data-language="R"><code class="language-R">df %&gt;% 
+  filter(!if_all(.fns = is.na))<span aria-hidden="true" class="line-numbers-rows"><span></span><span></span></span></code></pre></li>
+<li><p>用某一列做行名</p>
+<pre class="line-numbers language-R" data-language="R"><code class="language-R">df %&gt;% 
+  column_to_rownames()<span aria-hidden="true" class="line-numbers-rows"><span></span><span></span></span></code></pre></li>
+<li><p>对列重命名</p>
+<pre class="line-numbers language-R" data-language="R"><code class="language-R">df %&gt;% 
+  rename()<span aria-hidden="true" class="line-numbers-rows"><span></span><span></span></span></code></pre></li>
+</ul>
+<h1 id="分组处理"><a href="#分组处理" class="headerlink" title="分组处理"></a>分组处理</h1><pre class="line-numbers language-none"><code class="language-none">df %&gt;% 
+  group_by(group) %&gt;% 
+  summarise(count=n())<span aria-hidden="true" class="line-numbers-rows"><span></span><span></span><span></span></span></code></pre>
 
             </div>
             <hr/>

diff --git a/2023/04/21/Bioinfo-protein-structure-predict-and-visualize/index.html b/2023/04/21/Bioinfo-protein-structure-predict-and-visualize/index.html
@@ -406,7 +406,7 @@ <h1 class="description center-align post-title">蛋白质结构预测与可视
 
                 <div class="post-date info-break-policy">
                     <i class="far fa-calendar-check fa-fw"></i>更新日期:&nbsp;&nbsp;
-                    2024-02-22
+                    2024-03-14
                 </div>
 
 
@@ -470,6 +470,22 @@ <h2 id="使用-chimera-寻找结构差异"><a href="#使用-chimera-寻找结构
 
 <h1 id="PPI-互作分析："><a href="#PPI-互作分析：" class="headerlink" title="PPI 互作分析："></a>PPI 互作分析：</h1><p>可以使用 alphafold2-multimer 进行预测</p>
 <p><a target="_blank" rel="noopener" href="https://www.embopress.org/doi/full/10.15252/embr.202356834">An AlphaFold2 map of the 53BP1 pathway identifies a direct SHLD3–RIF1 interaction critical for shieldin activity</a></p>
+<h1 id="pymol-在-python-中的调用"><a href="#pymol-在-python-中的调用" class="headerlink" title="pymol 在 python 中的调用"></a>pymol 在 python 中的调用</h1><p>Pymol中很常用的一个包是cmd，在Python脚本中需要调用cmd来实现一些在命令窗口直接输入的命令。  </p>
+<p>比如: PyMOL&gt; select atom_c, name C这行命令在Python脚本中应写成cmd.select(‘atom_c’, ‘name C’)。  </p>
+<p>注：cmd.select(‘atom_c’, ‘name C’)可以在命令窗口中直接执行。</p>
+<pre class="line-numbers language-python" data-language="python"><code class="language-python"><span class="token keyword">from</span> pymol <span class="token keyword">import</span> cmd<span aria-hidden="true" class="line-numbers-rows"><span></span></span></code></pre>
+
+<h2 id="pymol-安装"><a href="#pymol-安装" class="headerlink" title="pymol 安装"></a>pymol 安装</h2><p>有<a target="_blank" rel="noopener" href="https://pymol.org/conda/">建议</a>是 这样安装: </p>
+<pre class="line-numbers language-bash" data-language="bash"><code class="language-bash">conda <span class="token function">install</span> -c conda-forge -c schrodinger pymol-bundle<span aria-hidden="true" class="line-numbers-rows"><span></span></span></code></pre>
+
+<p>但安装完成后，运行时出现了很多问题，找到了 pymol open source github 里面 [issue}(<a target="_blank" rel="noopener" href="https://github.com/schrodinger/pymol-open-source/issues/182">https://github.com/schrodinger/pymol-open-source/issues/182</a>) 提到：</p>
+<p>I removed pymol with <code>pip uninstall pymol</code> and <code>conda uninstall pymol</code>.<br>Re-installed pymol with <code>conda install -c conda-forge pymol-open-source</code></p>
+<p>另外的 issue 也提到了该<a target="_blank" rel="noopener" href="https://github.com/schrodinger/pymol-open-source/issues/304">解决思路</a></p>
+<p>操作步骤</p>
+<ol>
+<li>加载 pdb 文件: fetch 或 load （fetch 根据 pdb 的号，获取在线结构，load 加载本低文件）</li>
+<li>对 pdb object 进行操作，如 align</li>
+</ol>
 
 
             </div>

diff --git a/2024/03/01/API/index.html b/2024/03/01/API/index.html
@@ -7,7 +7,8 @@
     <meta name="keywords" content="利用 API 实现请求, Shaw">
     <meta name="description" content="API  代表应用程序编程接口。
 API 简介可参考各种资料。在这里，记录一下利用 curl 对 web tools 发送请求，实现简单利用 web tools。
-Uniprot ID mappinguniprot ID_mapping w">
+curlcurl options  
+Linux中使用curl命令发送带参数">
     <meta http-equiv="X-UA-Compatible" content="IE=edge">
     <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=no">
     <meta name="renderer" content="webkit|ie-stand|ie-comp">
@@ -391,7 +392,7 @@ <h1 class="description center-align post-title">利用 API 实现请求</h1>
 
                 <div class="post-date info-break-policy">
                     <i class="far fa-calendar-check fa-fw"></i>更新日期:&nbsp;&nbsp;
-                    2024-03-01
+                    2024-03-17
                 </div>
 
 
@@ -415,14 +416,18 @@ <h1 class="description center-align post-title">利用 API 实现请求</h1>
             <div id="articleContent">
                 <p>API  代表应用程序编程接口。</p>
 <p>API 简介可参考各种资料。在这里，记录一下利用 curl 对 web tools 发送请求，实现简单利用 web tools。</p>
+<h2 id="curl"><a href="#curl" class="headerlink" title="curl"></a>curl</h2><p><a target="_blank" rel="noopener" href="https://gist.github.com/subfuzion/08c5d85437d5d4f00e58">curl options</a>  </p>
+<p><a target="_blank" rel="noopener" href="https://blog.csdn.net/finghting321/article/details/105733140">Linux中使用curl命令发送带参数的get请求和post请求</a></p>
 <h2 id="Uniprot-ID-mapping"><a href="#Uniprot-ID-mapping" class="headerlink" title="Uniprot ID mapping"></a>Uniprot ID mapping</h2><p><a target="_blank" rel="noopener" href="https://www.uniprot.org/id-mapping/">uniprot ID_mapping web</a></p>
 <p>除了直接在页面上使用，也可以通过 API request，例如：指定好 ID mapping 前后的格式</p>
 <pre class="line-numbers language-bash" data-language="bash"><code class="language-bash"><span class="token function">curl</span> --form <span class="token string">'from="UniProtKB_AC-ID"'</span> <span class="token punctuation">\</span>
      --form <span class="token string">'to="Ensembl_Transcript"'</span> <span class="token punctuation">\</span>
      --form <span class="token string">'ids="P49815,P36888,P58215"'</span> <span class="token punctuation">\</span>
      https://rest.uniprot.org/idmapping/run<span aria-hidden="true" class="line-numbers-rows"><span></span><span></span><span></span><span></span></span></code></pre>
 
-<h2 id="ESMFold-predict"><a href="#ESMFold-predict" class="headerlink" title="ESMFold predict"></a>ESMFold predict</h2>
+<h2 id="ESMFold-predict"><a href="#ESMFold-predict" class="headerlink" title="ESMFold predict"></a>ESMFold predict</h2><pre class="line-numbers language-bash" data-language="bash"><code class="language-bash"><span class="token function">curl</span> -k -X POST --data <span class="token string">"MKSEDYPHETMAPDIHEERQYRCEDCDQLFESKAELADHQKFPCSTPHSAFSMVEEDFQQKLESENDLQEIHTIQECKECDQVFPDL"</span> https://api.esmatlas.com/foldSequence/v1/pdb/<span aria-hidden="true" class="line-numbers-rows"><span></span></span></code></pre>
+
+
 
             </div>
             <hr/>
@@ -797,18 +802,17 @@ <h2 id="ESMFold-predict"><a href="#ESMFold-predict" class="headerlink" title="ES
 <article id="prenext-posts" class="prev-next articles">
     <div class="row article-row">
 
-        <div class="article col s12 m6" data-aos="fade-up" data-aos="fade-up">
+        <div class="article col s12 m6" data-aos="fade-up">
             <div class="article-badge left-badge text-color">
-                <i class="far fa-dot-circle"></i>&nbsp;本篇
-            </div>
+                <i class="fas fa-chevron-left"></i>&nbsp;上一篇</div>
             <div class="card">
-                <a href="/2024/03/01/API/">
+                <a href="/2024/03/13/software-inistall/">
                     <div class="card-image">
 
 
-                        <img src="/medias/featureimages/9.jpg" class="responsive-img" alt="利用 API 实现请求">
+                        <img src="/medias/featureimages/19.jpg" class="responsive-img" alt="软件安装遇到的事儿">
 
-                        <span class="card-title">利用 API 实现请求</span>
+                        <span class="card-title">软件安装遇到的事儿</span>
                     </div>
                 </a>
                 <div class="card-content article-content">
@@ -818,9 +822,9 @@ <h2 id="ESMFold-predict"><a href="#ESMFold-predict" class="headerlink" title="ES
 
                     </div>
                     <div class="publish-info">
-                            <span class="publish-date">
-                                <i class="far fa-clock fa-fw icon-date"></i>2024-03-01
-                            </span>
+                        <span class="publish-date">
+                            <i class="far fa-clock fa-fw icon-date"></i>2024-03-13
+                        </span>
                         <span class="publish-author">
 
                             <i class="fas fa-user fa-fw"></i>
@@ -829,7 +833,6 @@ <h2 id="ESMFold-predict"><a href="#ESMFold-predict" class="headerlink" title="ES
                         </span>
                     </div>
                 </div>
-
 
             </div>
         </div>