{"id":572,"date":"2023-01-14T15:11:15","date_gmt":"2023-01-14T07:11:15","guid":{"rendered":"https:\/\/www.homechemer.com\/?p=572"},"modified":"2023-01-14T17:07:30","modified_gmt":"2023-01-14T09:07:30","slug":"supercell-py%e4%bb%8e%e5%8e%9f%e8%83%9e-cif%e5%bb%ba%e6%a8%a1%e8%b6%85%e8%83%9e-pdb","status":"publish","type":"post","link":"https:\/\/www.homechemer.com\/computchem\/8","title":{"rendered":"Supercell.py\uff1a\u4ece\u539f\u80de.cif\u5efa\u6a21\u8d85\u80de.pdb"},"content":{"rendered":"\n

Supercell.py\uff1a\u4ece\u539f\u80de.cif\u5efa\u6a21\u8d85\u80de.pdb
Supercell.py: From Unit Cell .cif to Super Cell .pdb<\/strong><\/p>\n\n\n\n

Jiawei Xu
Released: 2023-01-14 \/ Updated: 2023-01-14<\/p>\n\n\n\n

\u6269\u80de\u662f\u6750\u6599\u8ba1\u7b97\u4e2d\u65f6\u5e38\u4f1a\u9047\u5230\u7684\u6b65\u9aa4\u3002\u5e38\u89c1\u5e26\u6709\u5468\u671f\u6027\u4f53\u7cfb\u5efa\u6a21\u529f\u80fd\u7684\u8f6f\u4ef6\u5982GaussView\u3001Vesta\u3001Materials Studio\u3001VMD\u7b49\u90fd\u53ef\u4ee5\u8fdb\u884c\u6269\u80de\u64cd\u4f5c\u3002\u5728\u5206\u5b50\u52a8\u529b\u5b66\u548cQM\/MM\u8ba1\u7b97\u4e2d\uff0c\u6700\u5e38\u4f7f\u7528\u7684\u7ed3\u6784\u6587\u4ef6\u683c\u5f0f\u662f.pdb\uff0c\u8fd9\u4e0d\u80fd\u901a\u8fc7\u4ee5\u4e0a\u8f6f\u4ef6\u7531.cif\u6587\u4ef6\u65b9\u4fbf\u3001\u76f4\u63a5\u5730\u4ea7\u751f\u3002\u7b14\u8005\u662f\u5efa\u6a21\u7684\u61d2\u4eba\uff0c\u81f4\u529b\u4e8e\u4ee5\u6613\u7528\u7684GaussView\u4e3a\u4e3b\u5b8c\u6210\u5404\u79cd\u9700\u6c42\u7684\u5efa\u6a21\uff0c\u56e0\u6b64\u672c\u6587\u5c06\u901a\u8fc7\u4e00\u4e2a\u5b9e\u4f8b\u4ecb\u7ecdSupercell.py\u8fd9\u4e00\u5c0f\u7a0b\u5e8f\u7684\u4f7f\u7528\u65b9\u6cd5\uff0c\u8be5\u7a0b\u5e8f\u53ef\u4ece\u672c\u6587\u7ed3\u5c3e\u5904\u94fe\u63a5\u4e0b\u8f7d\u3002<\/p>\n\n\n\n

\u6211\u4eec\u4eceCOD\u4e0b\u8f7dID\u4e3a4024905\u7684\u6676\u4f53\u6587\u4ef6\uff0c\u8fd9\u662f\u4e00\u4e2aBODIPY\u884d\u751f\u7269\u7684\u7ed3\u6784\u3002\u7528GaussView\u6253\u5f00\u53ef\u770b\u5230\u4e00\u4e2a\u5355\u80de\u4e2d\u5305\u542b\u4e86\u53d6\u5411\u4e0d\u540c\u7684\u4e24\u4e2aBODIPY\u5206\u5b50\uff0c\u4e14\u5df2\u7ecf\u5305\u542b\u4e86\u6c22\u539f\u5b50\uff0c\u517180\u4e2a\u539f\u5b50\u3002\u9996\u5148\u7528VASP\u5bf9\u8be5\u7ed3\u6784\u8fdb\u884c\u7b80\u5355\u4f18\u5316\uff0c\u5c06\u6240\u5f97CONTCAR\u7528Vesta\u5bfc\u51fa\u4e3a.cif\u6587\u4ef6\uff0c\u7ed3\u6784\u548c\u6676\u80de\u53c2\u6570\u57fa\u672c\u6ca1\u6709\u53d1\u751f\u592a\u5927\u6539\u53d8\u3002\u5728GaussView\u4e2d\u6253\u5f00\u4f18\u5316\u540e\u7684\u7ed3\u6784\uff0c\u89c2\u5bdf\u53d1\u73b0\u5206\u5b50\u88ab\u5468\u671f\u6027\u8fb9\u754c\u622a\u65ad\uff0c\u8fd9\u4f1a\u5bfc\u81f4\u540e\u7eed\u5efa\u6a21\u65f6residue\u5b9a\u4e49\u51fa\u73b0\u95ee\u9898\uff0c\u4e5f\u4e0d\u80fd\u4fdd\u8bc1\u8d85\u80de\u8fb9\u754c\u4e0a\u5206\u5b50\u7684\u5b8c\u6574\u6027\u3002<\/p>\n\n\n\n

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\"\"<\/figure>\n<\/div>\n\n\n\n
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\"\"<\/figure>\n<\/div>\n<\/div>\n\n\n\n

\u9996\u5148\u5bf9\u5176\u5728GaussView\u4e2d\u6269\u80de\uff0c\u6784\u5efa3\u00d72\u00d72\u7684\u8d85\u80de\uff0c\u6b64\u65f6\u4fdd\u8bc1\u4e86\u8d85\u80de\u4e2d\u5fc3\u6709\u4e00\u5bf9\u5b8c\u6574\u7684\u5206\u5b50\uff0c\u70b9\u51fbCombine\u3002\u5bf9\u4e8e\u6027\u80fd\u4e00\u822c\u7684\u7b14\u8bb0\u672c\u6b64\u65f6\u4f1a\u6bd4\u8f83\u5361\u987f\uff0c\u4f46\u6211\u4eec\u5e76\u4e0d\u9700\u8981\u9488\u5bf9\u8fd9\u4e2a\u8d85\u80de\u5efa\u6a21\u3002\u9002\u5f53\u8c03\u6574\u89c6\u89d2\uff0c\u7528\u6846\u9009\u5de5\u5177\u5220\u9664\u5468\u56f4\u591a\u4f59\u7684\u5206\u5b50\uff0c\u53ea\u4fdd\u7559\u4e2d\u95f4\u4e00\u5bf9\u53d6\u5411\u4e0d\u540c\u7684\u5206\u5b50\u3002\u5220\u9664\u4e00\u6279\u540e\uff0c\u7531\u4e8e\u539f\u5b50\u6570\u53d8\u5c11\uff0c\u8f6c\u52a8\u4f1a\u66f4\u4e3a\u65b9\u4fbf\u3002\u4fdd\u5b58\u6700\u540e\u7684\u4e24\u4e2a\u5206\u5b50\u7684\u5750\u6807\u4e3a.gjf\u6587\u4ef6\u3002\u518d\u6b21\u6253\u5f00.cif\u6587\u4ef6\uff0c\u76f4\u63a5\u4fdd\u5b58\u4e3a\u53e6\u4e00\u4e2a.gjf\u6587\u4ef6\uff0c\u7136\u540e\u5c06\u524d\u9762\u7684\u5750\u6807\u66ff\u6362.cif\u5bfc\u51fa\u7684.gjf\u4e2d\u7684\u5750\u6807\uff0c\u6ce8\u610f\u4e0d\u8981\u6539\u52a8Tv\u7684\u5750\u6807\uff0c\u6253\u5f00\u540e\u53ef\u4ee5\u770b\u5230\u6b64\u65f6\u7684\u5206\u5b50\u5df2\u7ecf\u662f\u5b8c\u6574\u7684\uff0c\u7528\u5206\u5c42\u529f\u80fd\u8bb0\u5f55\u4e24\u4e2a\u5206\u5b50\u5404\u81ea\u7684\u539f\u5b50\u5e8f\u53f7\u3002\u5bf9\u4e8e\u672c\u4f8b\u5206\u522b\u662f1-26,41,44-56\u548c27-40,42-43,57-80\uff0c\u64cd\u4f5c\u4e0d\u540c\u53ef\u80fd\u6709\u6240\u533a\u522b\u3002\u81f3\u6b64\uff0c\u5efa\u6a21\u6e38\u620f\u5df2\u7ecf\u7ed3\u675f\u3002<\/p>\n\n\n\n

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\"\"<\/figure>\n<\/div>\n\n\n\n
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\"\"<\/figure>\n<\/div>\n<\/div>\n\n\n\n

\u6253\u5f00Supercell.py\u6587\u4ef6\uff0c\u4fee\u6539\u6587\u4ef6\u5f00\u5934extend\u548cresidues\u7684\u503c\u3002extend\u4e2d\u5b9a\u4e49\u4e86\u5411x+\u3001x-\u3001y+\u3001y-\u3001z+\u548cz-\u516d\u4e2a\u65b9\u5411\u6269\u80de\u7684\u8303\u56f4\uff0c\u5b9e\u9645\u4e0a\u53ea\u8981\u662f\u6574\u6570\u5747\u53ef\uff0c\u7a0b\u5e8f\u6784\u5efa\u8d85\u80de\u65f6\u53ea\u5173\u5fc3\u4e8c\u8005\u7684\u5dee\u503c\uff0c\u82e5(0, 0, 0)\u5305\u542b\u5728\u8be5\u8303\u56f4\u5185\u5219\u4f1a\u4fdd\u7559\u539f\u59cb\u5750\u6807\u4e0b\u7684\u5355\u80de\u3002\u5982\u679c\u4f60\u60f3\u6784\u5efa\u4e8c\u7ef4\u7684\u8d85\u80de\uff0c\u5c06\u67d0\u4e00\u65b9\u5411\u7684\u6570\u503c\u586b\u4e3a(0, 0)\u5373\u53ef\u3002residues\u4e2d\u5b9a\u4e49\u4e86\u6b8b\u57fa\u5305\u542b\u7684\u539f\u5b50\u5e8f\u53f7\u4ee5\u53ca\u6b8b\u57fa\u540d\uff0c\u5fc5\u987b\u5305\u542b\u5355\u80de\u4e2d\u7684\u6240\u6709\u539f\u5b50\uff0c\u4e14\u4e0d\u91cd\u4e0d\u6f0f\uff0c\u6b8b\u57fa\u540d\u5e94\u4fdd\u6301\u5728\u4e09\u4e2a\u5b57\u7b26\u4ee5\u5185\u3002<\/p>\n\n\n\n

\u8fd0\u884cpython Supercell.py 4024905.gjf 4024905.pdb<\/mark>\u3002\u7528VMD\u89c2\u770b\u6240\u5f97\u7684.pdb\u6587\u4ef6\u3002\u5bf9\u4e8e\u672c\u4f8b\uff0c\u6211\u4eec\u6269\u5efa9\u00d75\u00d75\u7684\u8d85\u80de\uff0c\u5373\u8bbe\u7f6eextend\u7684\u6570\u503c\u5206\u522b\u4e3a(-4, 4)\u3001(-2, 2)\u548c(-2, 2)\u3002\u7a0b\u5e8f\u8fd0\u884c\u65f6\u8f93\u51fa\u6709\u5173\u539f\u80de\u548c\u8d85\u80de\u5927\u5c0f\u7684\u4fe1\u606f\uff0c\u5e76\u6307\u51fa\u539f\u80de\u5728\u8d85\u80de\u4e2d\u7684\u6b8b\u57fa\u53f7\u662f225~226\u3002\u8fd9\u4e00\u4fe1\u606f\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u5728VMD\u4e2d\u914d\u5408.tcl\u811a\u672c\uff0c\u901a\u8fc7\u9009\u62e9\u8bed\u53e5\u5bfc\u51fa\u6838\u5fc3\u533a\u57df\u5468\u56f4\u4e00\u5b9a\u8303\u56f4\u7684\u539f\u5b50\u5e8f\u53f7\u6216\u6b8b\u57fa\u53f7\uff0c\u8fdb\u800c\u7528\u4e8e\u505aQM\/MM\u8ba1\u7b97\u3002<\/p>\n\n\n\n

\u5bf9\u4e8e\u9700\u8981\u6784\u5efa\u6709\u7f3a\u9677\u7684\u8d85\u80de\uff0c\u4e5f\u53ef\u4ee5\u901a\u8fc7\u7b80\u5355\u8ba1\u7b97\u5224\u65ad\u9700\u8981\u4fee\u6539\u54ea\u4e00\u4e2a\u6b8b\u57fa\u53f7\uff0c\u7136\u540e\u76f4\u63a5\u6253\u5f00.pdb\u4fee\u6539\u3001\u6216\u901a\u8fc7VMD\u9009\u533a\u4fdd\u5b58\u540e\u4fee\u6539\u5373\u53ef\u3002<\/p>\n\n\n\n

\u4e0b\u8f7d\u94fe\u63a5<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

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