{"id":114,"date":"2025-03-27T03:04:39","date_gmt":"2025-03-27T03:04:39","guid":{"rendered":"http:\/\/drtem.cn\/?p=114"},"modified":"2025-08-08T14:19:36","modified_gmt":"2025-08-08T06:19:36","slug":"sp-toolkits%ef%bc%9acryosparc%e4%b8%8erelion%e9%ab%98%e6%95%88%e4%ba%92%e8%bd%ac","status":"publish","type":"post","link":"https:\/\/www.drtem.cn\/en\/2025\/03\/27\/sp-toolkits%ef%bc%9acryosparc%e4%b8%8erelion%e9%ab%98%e6%95%88%e4%ba%92%e8%bd%ac\/","title":{"rendered":"SP Toolkits: Efficient Interconversion Between CryoSPARC and RELION"},"content":{"rendered":"

\u4e00\u3001SP Toolkits\u6982\u8ff0<\/b><\/strong><\/span><\/p>\n

SP Toolkits\u662f\u4e00\u6b3e\u96c6\u6210\u5de5\u5177\u7bb1\uff0c\u65e8\u5728\u7b80\u5316\u51b7\u51bb\u7535\u955c\u9886\u57df\u7684\u6570\u636e\u5904\u7406\u6d41\u7a0b\u3002\u8be5\u5de5\u5177\u5c06\u6570\u636e\u540c\u6b65\u3001\u683c\u5f0f\u8f6c\u6362\u548c\u6279\u91cf\u5904\u7406\u7b49<\/b><\/strong>\u591a\u4e2a\u5e38\u7528\u529f\u80fd\u6574\u5408\u5728\u4e00\u8d77\uff0c\u63d0\u4f9b\u7edf\u4e00\u7684\u64cd\u4f5c\u754c\u9762\uff0c\u51cf\u5c11\u4e86\u7528\u6237\u9891\u7e41\u5207\u6362\u8f6f\u4ef6\u7684\u65f6\u95f4\u6210\u672c\u3002\u5176\u4e2d\u7684PYEM\u6a21\u5757\u652f\u6301RELION\u4e0eCryoSPARC\u4e4b\u95f4\u7684\u9897\u7c92\u6570\u636e\u683c\u5f0f\u4e92\u8f6c\uff0c\u786e\u4fdd\u4e86\u9897\u7c92\u5750\u6807\u4fe1\u606f\u5728\u4e24\u4e2a\u8f6f\u4ef6\u4e4b\u95f4\u7684\u51c6\u786e\u4f20\u9012\u3002\u672c\u6587\u5c06\u8be6\u7ec6\u4ecb\u7ecd\u5176\u4f7f\u7528\u65b9\u6cd5\u53ca\u5e94\u7528\u573a\u666f\u3002<\/span><\/p>\n

\u4e8c\u3001PYEM\u6a21\u5757\u4f7f\u7528\u573a\u666f<\/b><\/strong><\/span><\/p>\n

PYEM\u6a21\u5757<\/b><\/strong>\u5206\u4e3a\u4e24\u4e2a\u4e3b\u8981\u90e8\u5206\uff1a\u201cFOR POLISHING<\/b><\/strong>\u201d\u548c\u201cFOR RBMC<\/b><\/strong>\u201d\uff0c\u5206\u522b\u5bf9\u5e94\u5728RELION<\/b><\/strong>\u00a0\u4e2d\u8fdb\u884c\u9897\u7c92\u7684Bayesian Polishing<\/b><\/strong>\u00a0\u4efb\u52a1\u548c\u5728CryoSPARC<\/b><\/strong>\u00a0\u8fdb\u884c\u9897\u7c92\u7684\u00a0Reference Based Motion Correction\u00a0<\/b><\/strong>\u4efb\u52a1\u4e24\u79cd\u60c5\u51b5\u3002\u4ece\u672c\u8d28\u4e0a\u6765\u8bf4\uff0c\u9897\u7c92\u7684\u8f6c\u6362\u662f\u5750\u6807\u4fe1\u606f\u5728RELION\u548cCryoSPARC\u4e24\u4e2a\u8f6f\u4ef6\u4e2d\u7684\u4f20\u9012\u3002<\/span><\/p>\n

    \n
  1. FOR POLISHING\uff1a<\/b><\/strong><\/span><\/li>\n<\/ol>\n

    \u573a\u666f\u4e00\uff1a\u9897\u7c92\u6587\u4ef6\u6765\u81eaRELION \u7684Particle Extraction \u4efb\u52a1\uff0c\u5728CryoSPARC \u4e2d\u8fdb\u884c\u4e863D Classification\u3001Homogenous Refinement \u6216 Heterogeneous Refinement\u4efb\u52a1\u540e\uff0c\u5e0c\u671b\u5c06\u7b5b\u9009\u51fa\u7684\u9897\u7c92\u4fe1\u606f\u8f6c\u6362\u4e3a.star\u683c\u5f0f\uff0c\u4ee5\u5bfc\u5165\u5230RELION\u8fdb\u884cBayesian Polishing\u3002\u8fd9\u79cd\u573a\u666f\u4e0b\uff0c\u9700\u8981\u5728CryoSPARC\u4e2d\u8fd0\u884c`Import Micrographs`\u4efb\u52a1\u4ee5\u5bfc\u5165RELION\u7684MotionCor\u7ed3\u679c\uff0c\u5e76\u5c06\u5176\u6307\u5b9a\u4e3a`Import Particle Stack`\u4efb\u52a1\u7684`Source Exposures`\uff0c<\/b><\/strong>\u4ece\u800c\u5c06\u9897\u7c92\u5750\u6807\u4fe1\u606f\u5199\u5165CryoSPARC\u7684cs\u6587\u4ef6<\/b><\/strong>\u3002<\/b><\/strong><\/span><\/p>\n

      \n
    1. \u8fdb\u5165\u201cFOR POLISHING\u201d\u9009\u9879\u5361<\/span><\/li>\n
    2. \u5728\u201cInitial Particles From\u201d\u9009\u62e9RELION<\/span><\/li>\n
    3. \u8bbe\u7f6eMovie Type\u4e3a\u539f\u59cb\u6570\u636e\u683c\u5f0f\uff08\u5982tif\uff0ctiff\uff0cmrc\u6216eer\uff09<\/span><\/li>\n
    4. Input File 1\uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c\u9009\u62e9\u9700\u8981\u8f6c\u6362\u7684particles.cs\u6587\u4ef6\u8def\u5f84\uff0c\u4f8b\u5982\/ssd\/20241119\/CS-20241119\/J66\/J66_*_particles.cs<\/span><\/li>\n
    5. Input File 2\uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c\u9009\u62e9\u9700\u8981\u8f6c\u6362\u7684particle_passthrough.cs \u6587\u4ef6\u7684\u8def\u5f84\uff0c\u4f8b\u5982\/ssd\/20241119\/CS-20241119\/J66\/J66_passthrough_particles_*.cs<\/span><\/li>\n
    6. Extract Star File \uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c \u9009\u62e9RELION \u751f\u6210\u7684\u9897\u7c92\u6587\u4ef6\uff0c\u4f8b\u5982\/ssd\/20241119\/Extract\/job00*\/particles.star<\/span><\/li>\n
    7. Output Star File\uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c\u9009\u62e9\u8f93\u51fa\u6587\u4ef6\u7684\u4fdd\u5b58\u8def\u5f84\uff0c\u5e76\u5728\u5f39\u51fa\u7a97\u53e3\u7684File name\u4e00\u680f\u63d0\u4f9b\u8f93\u51fa\u6587\u4ef6\u540d<\/span><\/li>\n
    8. \u8bbe\u7f6e\u4ee5\u4e0a\u53c2\u6570\u540e\u70b9\u51fbRUN\uff0c\u7a0b\u5e8f\u5c06\u5f00\u59cb\u6587\u4ef6\u8f6c\u6362\u5e76\u751f\u6210star \u6587\u4ef6<\/span><\/li>\n<\/ol>\n

      \u573a\u666f\u4e8c\uff1a\u9897\u7c92\u6587\u4ef6\u6765\u81eaCryoSPARC \u7684Particle Extraction \u4efb\u52a1\uff0c\u5728CryoSPARC \u4e2d\u8fdb\u884c\u4e862D Classification\u30013D Classification\u6216Refinement\u4efb\u52a1\u540e\uff0c\u5e0c\u671b\u5c06\u9897\u7c92\u5bfc\u5165RELION\u4e2d\u7ee7\u7eed\u5904\u7406\uff0c\u5e76\u5bf9\u9897\u7c92\u505aBayesian Polishing\u3002\u6b64\u573a\u666f\u4e0b\u5f97\u5230\u7684star\u6587\u4ef6\u5305\u542b\u4e86\u8f6c\u5316\u540e\u7684\u9897\u7c92\u5750\u6807\uff0c\u9700\u8981\u5728RELION\u4e2d\u505a\u9897\u7c92\u7684\u91cd\u65b0\u63d0\u53d6\uff0c\u56e0\u6b64\u8fd8\u9700\u5728RELION\u4e2d\u8fd0\u884cImport movies\u3001Motion Correction\u4efb\u52a1\uff0c\u4f5c\u4e3a`Particle Extraction`\u7684\u8f93\u5165(`Motion Correction`\u4f7f\u7528\u7684`Binning <\/b><\/strong>factor<\/b><\/strong>`\u4e0eCryoSPARC\u4e2d\u4fdd\u6301\u4e00\u81f4)\u3002<\/b><\/strong><\/span><\/p>\n

        \n
      1. \u8fdb\u5165\u201cFOR POLISHING\u201d\u9009\u9879\u5361<\/span><\/li>\n
      2. \u5728\u201cInitial Particles From\u201d\u9009\u62e9CryoSPARC<\/span><\/li>\n
      3. Movie Type\uff1a\u9009\u62e9\u539f\u59cb\u6570\u636e\u7684\u683c\u5f0f\uff1b\u5982\uff1atif, tiff, mrc \u6216 eer<\/span><\/li>\n
      4. Input File 1\uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\u9009\u62e9\u9700\u8981\u8f6c\u6362\u7684particles.cs \u6587\u4ef6\u7684\u8def\u5f84\uff0c \u4f8b\u5982\/ssd\/20241119\/CS-20241119\/J66\/J66_*_particles.cs<\/span><\/li>\n
      5. Input File 2\uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c\u9009\u62e9\u9700\u8981\u8f6c\u6362\u7684particle_passthrough.cs \u6587\u4ef6\u7684\u8def\u5f84\uff0c\u4f8b\u5982\/ssd\/20241119\/CS-20241119\/J66\/J66_passthrough_particles_*.cs<\/span><\/li>\n
      6. MotionCorr Star File\uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c\u9009\u62e9\u6765\u81eaRELION \u7684micrographs.star \u6587\u4ef6\uff0c\u4f8b\u5982\/ssd\/20241119\/MotionCorr\/job002\/corrected_micrographs.star<\/span><\/li>\n
      7. Output Star File\uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c\u9009\u62e9\u8f93\u51fa\u6587\u4ef6\u7684\u4fdd\u5b58\u8def\u5f84\uff0c\u5e76\u5728\u5f39\u51fa\u7a97\u53e3\u7684File name\u4e00\u680f\u63d0\u4f9b\u8f93\u51fa\u6587\u4ef6\u540d<\/span><\/li>\n
      8. \u8bbe\u7f6e\u4ee5\u4e0a\u53c2\u6570\u540e\u70b9\u51fbRUN\uff0c\u7a0b\u5e8f\u5c06\u5f00\u59cb\u8f6c\u6362\u5e76\u751f\u6210star \u6587\u4ef6<\/span><\/li>\n
      9. FOR RBMC\uff1a<\/b><\/strong><\/span><\/li>\n<\/ol>\n

        \u573a\u666f\u4e00\uff1a\u9897\u7c92\u6587\u4ef6\u6765\u81eaRELION \u7684Particle Extraction \u4efb\u52a1\uff0c\u5728\u8fdb\u884c\u4e86RELION\u7684Class2D\/3D\u6216Refine3D \u4efb\u52a1\u540e\uff0c\u5e0c\u671b\u5bfc\u5165CryoSPARC \u8fdb\u884cReference Based Motion Correction\u3002<\/b><\/strong><\/span><\/p>\n

        \u6b64\u573a\u666f\u4e0b\u5f97\u5230\u7684s<\/b><\/strong>tar<\/b><\/strong>\u6587\u4ef6\u5305\u542b\u4e86\u9897\u7c92<\/b><\/strong>\u7684<\/b><\/strong>\u5750\u6807<\/b><\/strong>\u548cCTF\u7b49\u4fe1\u606f\uff0c\u5bfc\u5165CryoSPARC\u540e\u9700\u8981\u505a\u9897\u7c92\u7684\u91cd\u65b0\u63d0\u53d6(`<\/b><\/strong>Extract From Micrographs<\/b><\/strong>`)\u3002\u56e0\u6b64\u8fd8\u9700\u5728CryoSPARC \u4e2d\u8fd0\u884cImport movies \u548cPatch Motion Correction(\u4f7f\u7528\u4e0eRELION\u4e2d\u76f8\u540c\u7684`Binning <\/b><\/strong>factor<\/b><\/strong>`)\uff0c\u4f5c\u4e3a`<\/b><\/strong>Import Particle Stack<\/b><\/strong>`[\u6ce81]\u3001`<\/b><\/strong>Extract From Micrographs<\/b><\/strong>`\u548cReference Based Motion Correction \u7b49\u4efb\u52a1\u7684\u8f93\u5165\u3002<\/b><\/strong><\/span><\/p>\n

          \n
        1. \u8fdb\u5165\u201cFOR RBMC\u201d\u9009\u9879\u5361<\/span><\/li>\n
        2. \u5728\u201cInitial Particles From\u201d\u9009\u62e9RELION<\/span><\/li>\n
        3. Movie Type\uff1a\u9009\u62e9\u539f\u59cb\u6570\u636e\u7684\u683c\u5f0f\uff0c\u5982\uff1atif\uff0ctiff\uff0cmrc \u6216eer<\/span><\/li>\n
        4. Input File 3\uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c\u9009\u62e9\u9700\u8981\u8f6c\u6362\u5750\u6807\u7684\u9897\u7c92\u6587\u4ef6\uff0c\u5982\/ssd\/20241119\/Refine3D\/job028\/run_it000_data.star<\/span><\/li>\n
        5. Output Star File\uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c\u9009\u62e9RELION\u7684project\u6240\u5728\u8def\u5f84\uff0c\u5e76\u5728\u5f39\u51fa\u7a97\u53e3\u7684File name\u4e00\u680f\u63d0\u4f9b\u8f93\u51fa\u6587\u4ef6\u540d\uff0c\u4f8b\u5982\/ssd\/20241119\/test.star<\/span><\/li>\n
        6. \u8bbe\u7f6e\u4ee5\u4e0a\u53c2\u6570\u540e\u70b9\u51fbRUN\uff0c\u7a0b\u5e8f\u5c06\u5f00\u59cb\u5750\u6807\u8f6c\u6362\u5e76\u751f\u6210star\u6587\u4ef6\u3002\u6b64\u6587\u4ef6\u9700\u8981\u7528\u6237\u5728CryoSPARC\u4e2d\u4f7f\u7528Import Particle Stack\u4efb\u52a1\u5bfc\u5165\uff0c\u5e76\u63d0\u4f9bPatch Motion Correction\u4f5c\u4e3aImport Particle Stack\u7684Source Exposures<\/span><\/li>\n<\/ol>\n

          \u6ce81\uff1a\u4ee5CryoSPARC 4.6.2\u4e3a\u4f8b\uff0c\u4e3a\u4e86\u4f7f\u9897\u7c92\u5750\u6807\u4e0e\u7167\u7247\u6b63\u786e\u5339\u914d\uff0c\u9700\u8981\u5728CryoSPARC\u7684`Import Particle Stack`\u4efb\u52a1\u4e2d\u8fde\u63a5`Patch Motion\u00a0Correction`\u4f5c\u4e3a`Source Exposures`\uff0c\u7136\u540e\uff1aa.\u586b\u5165\u9897\u7c92star\u6587\u4ef6\uff1bb.\u5f00\u542f`Remove leading UID in input exposure file name`\u9009\u9879\u4ee5\u5ffd\u7565CryoSPARC\u4e3amicrographs\u6dfb\u52a0\u7684\u524d\u7f00UID\uff1bc.\u5728`Length of input exposure file name suffix to cut`\u586b\u516531\u4ee5\u79fb\u9664CryoSPARC\u751f\u6210\u7684\u6587\u4ef6\u540d\u540e\u7f00`patch_aligned_doseweighted.mrc`\uff1bd.\u5728`Length of rlnMicrographName base name suffix to cut for query`\u586b\u51654\u4ee5\u79fb\u9664star\u6587\u4ef6\u4e2d`rlnMicrographName`\u7684\u540e\u7f00`.mrc`\uff0c\u4ee5\u4e0a\u53c2\u6570\u586b\u5199\u540e\u5373\u53efqueue\u63d0\u4ea4\u4efb\u52a1\u3002<\/span><\/p>\n

          \u573a\u666f\u4e8c\uff1a\u9897\u7c92\u6587\u4ef6\u6765\u81eaCryoSPARC \u7684Particle Extraction \u4efb\u52a1\uff0c<\/b><\/strong>\u5e0c\u671b<\/b><\/strong>\u5728RELION \u4e2d<\/b><\/strong>\u505a<\/b><\/strong>Class2D\u6216Class3D\u8fdb\u884c\u9897\u7c92\u7b5b\u9009\uff0c\u800c\u540e\u7eed\u8fd8\u9700\u8981\u56de\u5230CryoSPARC\u505aReference Based Motion Correction<\/b><\/strong>\uff0c<\/b><\/strong>\u8fd9\u65f6\u65e0\u9700\u5728RELION\u4e2d\u91cd\u65b0\u63d0\u53d6\u9897\u7c92\uff0c\u53ea\u9700\u8981\u5c06`.cs`\u6587\u4ef6\u8f6c\u6362\u4e3a`.star`\u6587\u4ef6\u5e76\u5bf9CryoSPARC\u7684\u9897\u7c92\u521b\u5efa\u8f6f\u94fe\u63a5\u3002<\/b><\/strong><\/span><\/p>\n

            \n
          1. \u8fdb\u5165\u201cFOR RBMC\u201d\u9009\u9879\u5361<\/span><\/li>\n
          2. \u5728\u201cInitial Particles From\u201d\u9009\u62e9CryoSPARC<\/span><\/li>\n
          3. Movie Type\uff1a\u9009\u62e9\u539f\u59cb\u6570\u636e\u7684\u683c\u5f0f\uff0c\u5982\uff1atif\uff0ctiff\uff0cmrc \u6216eer<\/span><\/li>\n
          4. Input File 1 \uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c \u9009\u62e9\u9700\u8981\u8f6c\u6362\u7684particles.cs \u6587\u4ef6\u7684\u8def\u5f84\uff0c \u4f8b\u5982\/ssd\/20241119\/CS-20241119\/J66\/J66_*_particles.cs<\/span><\/li>\n
          5. Input File 2\uff1a\u70b9\u51fb\u6587\u4ef6\u5939\u56fe\u6807\uff0c\u9009\u62e9\u9700\u8981\u8f6c\u6362\u7684particle_passthrough.cs \u6587\u4ef6\u7684\u8def\u5f84\uff0c\u4f8b\u5982\/ssd\/20241119\/CS-20241119\/J66\/J66_passthrough_particles_*.cs<\/span><\/li>\n
          6. Create Particle Links\uff1a\u9009\u62e9\u662f\u5426\u9700\u8981\u7a0b\u5e8f\u540c\u65f6\u521b\u5efa\u9897\u7c92\u8f6f\u94fe\u63a5\uff0c\u9009\u62e9Yes\u5219\u5c06\u5728\u8f93\u51fa\u76ee\u5f55\u751f\u6210\u5f62\u5f0f\u4e3aJ*\/extract\/*.mrcs\u7684\u9897\u7c92\u8f6f\u94fe\u63a5<\/span><\/li>\n
          7. Output Star File\uff1a\u9009\u62e9RELION \u7684project \u6240\u5728\u8def\u5f84\uff0c\u5e76\u5728\u5f39\u51fa\u7a97\u53e3\u7684File name \u4e00\u680f\u63d0\u4f9b\u8f93\u51fa\u6587\u4ef6\u540d<\/span><\/li>\n
          8. \u8bbe\u7f6e\u4ee5\u4e0a\u53c2\u6570\u540e\u70b9\u51fbRUN\uff0c\u7a0b\u5e8f\u5c06\u5728\u63d0\u4f9b\u7684project \u76ee\u5f55\u751f\u6210star \u6587\u4ef6<\/span><\/li>\n<\/ol>\n

            \u4e09\u3001\u603b\u7ed3\u4e0e\u5c55\u671b<\/b><\/strong><\/span><\/p>\n

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