{"id":61126,"date":"2024-10-17T11:03:01","date_gmt":"2024-10-17T03:03:01","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61126"},"modified":"2024-10-17T11:03:01","modified_gmt":"2024-10-17T03:03:01","slug":"%e9%94%99%e8%bf%87%e7%9c%9f%e7%9a%84%e4%bc%9a%e5%90%8e%e6%82%94%ef%bc%81%e4%b8%89%e5%88%86%e9%92%9f%e6%95%99%e4%bc%9a%e4%bd%a0%e7%94%a8pymol%e6%b7%b1%e5%ba%a6%e8%a7%a3%e6%9e%90%e8%9b%8b%e7%99%bd","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61126","title":{"rendered":"\u9519\u8fc7\u771f\u7684\u4f1a\u540e\u6094\uff01\u4e09\u5206\u949f\u6559\u4f1a\u4f60\u7528PyMol\u6df1\u5ea6\u89e3\u6790\u86cb\u767d\u8d28\u4e0eDNA\u7684\u4e09\u7ef4\u7ed3\u6784\uff01"},"content":{"rendered":"\n
\"\"<\/figure>\n\n\n\n

\u540c\u5b66\u4eec\uff0c\u4eca\u5929\u5927\u6d77\u54e5\u8981\u5411\u5927\u5bb6\u4ecb\u7ecd\u4e00\u6b3e\u5728\u751f\u7269\u4fe1\u606f\u5b66\u548c\u7ed3\u6784\u751f\u7269\u5b66\u7814\u7a76\u4e2d\u975e\u5e38\u91cd\u8981\u7684\u5de5\u5177\u2014\u2014PyMOL\uff01\u53ea\u8981\u6211\u4eec\u9700\u8981\u7406\u89e3\u86cb\u767d\u8d28\u548c\u6838\u9178\u7684\u4e09\u7ef4\u7ed3\u6784\uff0c\u63ed\u793a\u5b83\u4eec\u5728\u7ec6\u80de\u5185\u7684\u529f\u80fd\u548c\u76f8\u4e92\u4f5c\u7528\uff0c\u5c31\u79bb\u4e0d\u5f00PyMOL\u7684\u5e2e\u52a9\u3002\u4f5c\u4e3a\u4e00\u6b3e\u5f3a\u5927\u7684\u5206\u5b50\u7ed3\u6784\u53ef\u89c6\u5316\u8f6f\u4ef6\uff0cPyMOL\u80fd\u591f\u4ee5\u9ad8\u5206\u8fa8\u7387\u5c55\u793a\u590d\u6742\u7684\u751f\u7269\u5927\u5206\u5b50\u7ed3\u6784\uff0c\u5e2e\u52a9\u6211\u4eec\u66f4\u597d\u5730\u7406\u89e3\u8fd9\u4e9b\u5206\u5b50\u5728\u751f\u7269\u8fc7\u7a0b\u4e2d\u7684\u5173\u952e\u4f5c\u7528\u3002\u901a\u8fc7PyMOL\uff0c\u6211\u4eec\u53ef\u4ee5\u8f7b\u677e\u5730\u5904\u7406\u548c\u5206\u6790\u8fd9\u4e9b\u7ed3\u6784\u6570\u636e\uff0c\u4e3a\u6211\u4eec\u7684\u79d1\u7814\u5de5\u4f5c\u63d0\u4f9b\u575a\u5b9e\u7684\u652f\u6301\u3002\u5927\u6d77\u54e5\u53ef\u662f\u62e5\u6709\u4e30\u5bcc\u7ecf\u9a8c\u7684\u751f\u4fe1\u9ad8\u624b\u54e6\uff0c\u5982\u679c\u540c\u5b66\u4eec\u6709\u4efb\u4f55\u751f\u4fe1\u5206\u6790\u65b9\u9762\u7684\u95ee\u9898\uff0c\u6b22\u8fce\u968f\u65f6\u8054\u7cfb\u6211\uff01<\/strong><\/strong><\/p>\n\n\n\n

\u5728\u672c\u6b21\u5b66\u4e60\u4e2d\uff0c\u5927\u6d77\u54e5\u5c06\u7ec6\u81f4\u5730\u6559\u5927\u5bb6\u5982\u4f55\u5b89\u88c5\u548c\u4f7f\u7528PyMOL\uff0c\u5e76\u901a\u8fc7\u5b9e\u9645\u793a\u4f8b\u7684\u6f14\u793a\uff0c\u8ba9\u540c\u5b66\u4eec\u66f4\u6df1\u5165\u5730\u4e86\u89e3\u5982\u4f55\u8fdb\u884c\u5206\u5b50\u7ed3\u6784\u7684\u53ef\u89c6\u5316\u5206\u6790\u3002\u56e0\u6b64\uff0c\u672c\u6b21\u5b66\u4e60\u5bf9\u5927\u5bb6\u6765\u8bf4\u5341\u5206\u91cd\u8981\uff0c\u5e0c\u671b\u540c\u5b66\u4eec\u8ba4\u771f\u542c\u8bb2\u5e76\u79ef\u6781\u52a8\u624b\u5b9e\u8df5\u3002\u5927\u6d77\u54e5\u76f8\u4fe1\uff0c\u901a\u8fc7\u8fd9\u6b21\u5b66\u4e60\uff0c\u540c\u5b66\u4eec\u4e0d\u4ec5\u80fd\u638c\u63e1PyMOL\u7684\u4f7f\u7528\u6280\u5de7\uff0c\u8fd8\u80fd\u66f4\u6df1\u5165\u5730\u7406\u89e3\u751f\u7269\u5927\u5206\u5b50\u7684\u7ed3\u6784\u548c\u529f\u80fd\uff0c\u4e3a\u4eca\u540e\u7684\u79d1\u7814\u5de5\u4f5c\u6253\u4e0b\u575a\u5b9e\u7684\u57fa\u7840\u3002<\/p>\n\n\n\n

\u672c\u6b21\u4ecb\u7ecd\u7684\u5de5\u5177\u9700\u8981\u5728<\/strong>\u670d\u52a1\u5668<\/strong>\u4e0a\u624d\u80fd\u6b63\u5e38<\/strong>\u8fd0\u884c\uff0c<\/strong>\u540c\u5b66\u4eec<\/strong>\u5982\u679c\u6ca1\u6709\u81ea\u5df1\u7684\u670d\u52a1\u5668\u6b22\u8fce\u8054\u7cfb\u6211\u4eec<\/strong>\u8fdb\u884c<\/strong>\u670d\u52a1\u5668\u79df\u8d41~<\/strong><\/strong><\/p>\n\n\n\n

PyMol\u7684\u4ecb\u7ecd<\/p>\n\n\n\n

PyMOL \u662f\u4e00\u6b3e\u5e7f\u6cdb\u5e94\u7528\u4e8e\u5206\u5b50\u7ed3\u6784\u53ef\u89c6\u5316\u7684\u5f00\u6e90\u8f6f\u4ef6\uff0c\u7279\u522b\u9002\u7528\u4e8e\u751f\u7269\u5316\u5b66\u548c\u751f\u7269\u7269\u7406\u5b66\u7814\u7a76\u3002\u5b83\u80fd\u591f\u4ee5\u9ad8\u5206\u8fa8\u7387\u663e\u793a\u86cb\u767d\u8d28\u3001\u6838\u9178\u7b49\u751f\u7269\u5927\u5206\u5b50\u7684\u4e09\u7ef4\u7ed3\u6784\uff0c\u652f\u6301\u591a\u79cd\u6587\u4ef6\u683c\u5f0f\u5982PDB\u548cCIF\u3002\u7528\u6237\u53ef\u4ee5\u901a\u8fc7\u76f4\u89c2\u7684\u56fe\u5f62\u754c\u9762\u6216\u7075\u6d3b\u7684\u547d\u4ee4\u884c\u5de5\u5177\u8fdb\u884c\u5206\u5b50\u5efa\u6a21\u548c\u5206\u6790\uff0c\u5305\u62ec\u65cb\u8f6c\u3001\u5e73\u79fb\u548c\u7f29\u653e\u7ed3\u6784\uff0c\u4ee5\u53ca\u663e\u793a\u6c22\u952e\u7b49\u751f\u7269\u5206\u5b50\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u3002PyMOL \u63d0\u4f9b\u5f3a\u5927\u7684\u6e32\u67d3\u529f\u80fd\uff0c\u751f\u6210\u9ad8\u8d28\u91cf\u7684\u9759\u6001\u56fe\u50cf\u548c\u52a8\u6001\u52a8\u753b\uff0c\u9002\u7528\u4e8e\u79d1\u7814\u3001\u6559\u5b66\u548c\u5b66\u672f\u6f14\u793a\u3002<\/p>\n\n\n\n

PyMol\u5b89\u88c5<\/p>\n\n\n\n

\u9996\u5148\uff0c\u6253\u5f00\u4f60\u7684\u6d4f\u89c8\u5668\uff0c\u8bbf\u95eePyMOL\u7684\u5b98\u65b9\u7f51\u7ad9\uff08https:\/\/PyMol.org\/2\/\uff09\u3002\u5728\u4e3b\u9875\u4e0a\uff0c\u4f60\u4f1a\u770b\u5230\u201cDownload\u201d\u6309\u94ae\uff0c\u70b9\u51fb\u5b83\u8fdb\u5165\u4e0b\u8f7d\u9875\u9762\u3002\u5728\u8fd9\u91cc\uff0c\u4f60\u53ef\u4ee5\u9009\u62e9\u9002\u5408\u4f60\u64cd\u4f5c\u7cfb\u7edf\u7684\u7248\u672c\u8fdb\u884c\u4e0b\u8f7d\u3002PyMOL\u652f\u6301Windows\u3001MacOS\u548cLinux\u7cfb\u7edf\uff0c\u6240\u4ee5\u4e0d\u7ba1\u4f60\u7528\u7684\u662f\u54ea\u79cd\u7535\u8111\uff0c\u90fd\u53ef\u4ee5\u627e\u5230\u5bf9\u5e94\u7684\u5b89\u88c5\u5305\u3002<\/p>\n\n\n\n

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

\u4e0b\u8f7d\u5b8c\u6210\u540e\uff0c\u53cc\u51fb\u5b89\u88c5\u5305\u5f00\u59cb\u5b89\u88c5\u3002\u5b89\u88c5\u8fc7\u7a0b\u5f88\u7b80\u5355\uff0c\u53ea\u9700\u8981\u6309\u7167\u63d0\u793a\u70b9\u51fb\u201cNext\u201d\u5c31\u53ef\u4ee5\u4e86\u3002\u9700\u8981\u6ce8\u610f\u7684\u662f\uff0c\u5982\u679c\u4f60\u4f7f\u7528\u7684\u662fWindows\u7cfb\u7edf\uff0c\u5728\u5b89\u88c5\u8fc7\u7a0b\u4e2d\u53ef\u80fd\u4f1a\u63d0\u793a\u4f60\u5b89\u88c5\u4e00\u4e9b\u5fc5\u8981\u7684\u4f9d\u8d56\u7ec4\u4ef6\uff0c\u6309\u7167\u63d0\u793a\u5b89\u88c5\u5373\u53ef\u3002<\/p>\n\n\n\n

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

\u6210\u529f\u5b89\u88c5\u4e4b\u540e\uff0cPyMol\u7684\u754c\u9762\u5982\u56fe\u6240\u793a\uff1a<\/p>\n\n\n\n

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

\u4f7f\u7528PyMol\u8fdb\u884c\u5206\u5b50\u7ed3\u6784\u53ef\u89c6\u5316\u5206\u6790<\/p>\n\n\n\n

\u6587\u4ef6\u8f7d\u5165<\/strong><\/strong><\/p>\n\n\n\n

\u5728\u672c\u6587\u4e2d\uff0c\u5927\u6d77\u54e5\u5c06\u4f7f\u7528\u8f6c\u5f55\u56e0\u5b50\u548cDNA\u7ed3\u5408\u7684\u590d\u5408\u7269\u7684\u4e09\u7ef4\u7ed3\u6784\u5411\u5927\u5bb6\u6f14\u793a\u5982\u4f55\u4f7f\u7528PyMol\u8fdb\u884c\u5206\u5b50\u7ed3\u6784\u53ef\u89c6\u5316\u5206\u6790\u3002\u5927\u6d77\u54e5\u5df2\u7ecf\u51c6\u5907\u597d\u4e86\u8f6c\u5f55\u56e0\u5b50\uff08General transcription factor IIH subunit 4\uff09\u548cDNA\u5206\u5b50\u7684\u793a\u4f8b\u6587\u4ef6\uff08example.pdb\uff09\uff0c\u540c\u5b66\u4eec\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528\u3002\u9996\u5148\u6253\u5f00 PyMOL \u8f6f\u4ef6\u3002\u5728\u754c\u9762\u4e0a\u65b9\u7684\u83dc\u5355\u680f\u4e2d\uff0c\u9009\u62e9\u201cFile\u201d -> \u201cOpen\u201d\u6765\u52a0\u8f7dexample.PDB \u6587\u4ef6,PyMOL \u5c06\u81ea\u52a8\u52a0\u8f7d\u5e76\u663e\u793a\u86cb\u767d\u8d28\u7684\u4e09\u7ef4\u7ed3\u6784\u3002<\/p>\n\n\n\n

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

\u7ed3\u679c\u663e\u793a\u5982\u4e0a\u56fe\uff0c\u540c\u5b66\u4eec\u53ef\u4ee5\u4f7f\u7528\u9f20\u6807\u5de6\u952e\u62d6\u52a8\u6765\u65cb\u8f6c\u5206\u5b50\uff0c\u53f3\u952e\u62d6\u52a8\u6765\u5e73\u79fb\u5206\u5b50\uff0c\u6eda\u52a8\u9f20\u6807\u6eda\u8f6e\u6765\u7f29\u653e\u5206\u5b50\u7684\u5927\u5c0f\u3002\u8fd9\u4e9b\u64cd\u4f5c\u80fd\u591f\u5e2e\u52a9\u6211\u4eec\u66f4\u5168\u9762\u5730\u89c2\u5bdf\u548c\u5206\u6790\u86cb\u767d\u8d28\u4e0e DNA \u7ed3\u6784\u590d\u5408\u4f53\u7684\u5404\u4e2a\u65b9\u9762\u3002<\/p>\n\n\n\n

\u86cb\u767d\u8d28\u4e0eDNA\u7ed3\u5408\u89e3\u6790<\/strong><\/strong><\/p>\n\n\n\n

\u901a\u8fc7\u4ee5\u4e0a\u7684\u6b65\u9aa4\uff0c\u867d\u7136\u86cb\u767d\u8d28\u548c\u6c28\u57fa\u9178\u7ed3\u6784\u88ab\u6e05\u6670\u663e\u793a\u51fa\u6765\uff0c\u4f46\u662f\u4e24\u8005\u4e4b\u95f4\u7684\u7ed3\u5408\u5173\u7cfb\u8fd8\u4e0d\u591f\u660e\u786e\u3002\u63a5\u4e0b\u6765\uff0c\u8ba9\u6211\u4eec\u9009\u4e2d\u86cb\u767d\u8d28\uff0c\u5728\u53f3\u8fb9\u7684\u72b6\u6001\u680f\u4e2d\uff08sele\uff09\u9879\u76ee\u4e2d\u9009\u62e9\u201dA\u201d->\u201dfind\u201d->\u201dpolar contacts\u201d->\u201dto other atoms in object\u201d\u3002<\/p>\n\n\n\n

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

\u81f3\u6b64\u5c31\u6210\u529f\u663e\u793a\u4e86\u86cb\u767d\u8d28\u548cDNA\u76f8\u4e92\u94fe\u63a5\u7684\u6c22\u952e\u4e86\uff0c\u968f\u540e\u6211\u4eec\u628a\u86cb\u767d\u8d28\u5355\u72ec\u51fa\u63d0\u53d6\u51fa\u6765\uff0c\u5e76\u8bbe\u7f6e\u4e3asurface\u6a21\u5f0f\u663e\u793a\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

extract protein, example and chain V #\u5355\u72ec\u63d0\u53d6\u86cb\u767d\u8d28<\/p>\n\n\n\n

cmd.show_as(“surface”,”protein”) #\u8bbe\u7f6e\u86cb\u767d\u8d28\u4e3asurface\u663e\u793a<\/p>\n\n\n\n

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

\u663e\u793a\u5982\u4e0a\u56fe\uff0c\u5176\u4e2d\u9ec4\u8272\u865a\u7ebf\u5373\u4e3a\u4e24\u8005\u4e4b\u95f4\u5f62\u6210\u7684\u6c22\u952e\u3002\u4e3a\u4e86\u8ba9\u7ed3\u679c\u66f4\u52a0\u76f4\u89c2\u6e05\u6670\uff0c\u6211\u4eec\u53ef\u4ee5\u8c03\u6574PyMol\u7684\u4e00\u4e9b\u53c2\u6570\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

# \u8bbe\u7f6e\u80cc\u666f\u989c\u8272\u4e3a\u767d\u8272<\/p>\n\n\n\n

bg_color white<\/p>\n\n\n\n

# \u8bbe\u7f6e\u5149\u7ebf\u8ffd\u8e2a\u76f8\u5173\u53c2\u6570<\/p>\n\n\n\n

set ray_trace_gain, 0.1<\/p>\n\n\n\n

set ray_trace_discoeff, 0.1<\/p>\n\n\n\n

set ray_trace_mode, 1<\/p>\n\n\n\n

set ray_shadows, 1<\/p>\n\n\n\n

# \u8bbe\u7f6e\u5149\u7167\u6548\u679c<\/p>\n\n\n\n

set ambient, 0.3<\/p>\n\n\n\n

set specular, 0.5<\/p>\n\n\n\n

set shininess, 75<\/p>\n\n\n\n

set spec_direct, 0.3<\/p>\n\n\n\n

set spec_direct_power, 200<\/p>\n\n\n\n

set reflect, 0.2<\/p>\n\n\n\n

# \u8bbe\u7f6e\u6297\u952f\u9f7f<\/p>\n\n\n\n

set antialias, 2<\/p>\n\n\n\n

# \u8c03\u6574\u9634\u5f71\u548c\u900f\u660e\u5ea6\u7684\u7cbe\u5ea6<\/p>\n\n\n\n

set ray_shadow, 1<\/p>\n\n\n\n

set ray_transparency_shadows, 1<\/p>\n\n\n\n

set ray_interior_shadows, 1<\/p>\n\n\n\n

set ray_trace_depth, 4<\/p>\n\n\n\n

# \u5173\u95ed\u6df1\u5ea6\u63d0\u793a\u548c\u5149\u7ebf\u8ffd\u8e2a\u96fe<\/p>\n\n\n\n

set depth_cue, 0<\/p>\n\n\n\n

set ray_trace_fog, 0<\/p>\n\n\n\n

\u968f\u540e\u8c03\u6574\u597d\u5408\u9002\u7684\u753b\u9762\u89d2\u5ea6\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u6e32\u67d3\u56fe\u50cf\u5e76\u4fdd\u5b58\uff0c\u547d\u4ee4\u5982\u4e0b\uff1a<\/p>\n\n\n\n

ray 2000, 2000 #\u8fdb\u884c\u6e32\u67d3<\/p>\n\n\n\n

\u8fd9\u4e2a\u8fc7\u7a0b\u53ef\u80fd\u9700\u8981\u6d88\u8017\u4e00\u4e9b\u65f6\u95f4\uff0c\u5927\u5bb6\u9700\u8981\u8010\u5fc3\u7b49\u5f85\u4e00\u4e0b\uff0c\u52a0\u8f7d\u5b8c\u6210\u4e4b\u540e\uff0c\u4f9d\u6b21\u9009\u62e9\u201cFile\u201d->\u201dExport Image As\u201d->\u201dPNG\u201d\u3002<\/p>\n\n\n\n

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

\u6e32\u67d3\u7ed3\u679c\u89e3\u6790\uff1a<\/strong><\/strong><\/p>\n\n\n\n

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

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