scipion-em-eman2 1.0.5

安装

您需要使用2.0版本的scipion才能运行这些协议。要安装插件，有两个选项：

1. 稳定版本

scipion installp -p scipion-em-eman2

1. 开发人员版本

   • download repository

   git clone https://github.com/scipion-em/scipion-em-eman2.git
   

   • install

   scipion installp -p path_to_scipion-em-eman2 --devel
   

EnM2二进制文件将自动安装在插件中，但您也可以链接现有的安装。

• Default installation path assumed is ^{tt1}$, if you want to change it, set EMAN2_HOME in ^{tt2}$ file pointing to the folder where the EMAN2 is installed.

IMPORTANT: From plugin version 1.0.5 EMAN2DIR was renamed to EMAN2_HOME. Please update your scipion.conf file!

• If you need to pass special options to mpirun (like a hostfile), you can use the EMANMPIOPTS shell variable, but most users should not need this. A typical usage would be ^{tt3}$. You should only do this if necessary, though (note that then when supplying the parameter –parallel=mpi:n:scratch_directory, ‘n’ is no longer the number of cpus to use, but rather the number of nodes listed in myhosts.txt).
• The default scratch directory is assumed /tmp/. You can change it by setting EMAN2SCRATCHDIR in your shell environment.

要检查安装，只需运行以下scipion测试之一：

scipion test eman2.tests.test_protocols_eman.TestEmanTiltValidate
scipion test eman2.tests.test_protocols_eman.TestEmanRefineEasy
scipion test eman2.tests.test_protocols_eman.TestEmanRefine2DBispec
scipion test eman2.tests.test_protocols_eman.TestEmanRefine2D
scipion test eman2.tests.test_protocols_eman.TestEmanReconstruct
scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelMda
scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelGroel
scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelSGD
scipion test eman2.tests.test_protocols_eman.TestEmanCtfAuto
scipion test eman2.tests.test_protocols_eman.TestEmanAutopick

执行scipion test --show--grep eman

支持的版本

2.21，2.3

2018年，插件更新为支持最新版本（当时）的eman2:2.21。这需要大量的代码重构，旧的eman2版本2.11的支持不得不停止。增加了一些新的协议：2d改进、倾斜验证、ctf自动和新的e2boxer。scipion-1.x之后的完整变更日志可用here。

协议

• boxer (old and new interactive e2boxer.py)
• Boxer Auto（全自动新Boxer in>；=2.21）
• CTF自动
• initial model
• 初始型号SGD
• 重建
• 优化二维
• 细化二维二次曲线
• 轻松优化
• sparx picker
• 倾斜验证

参考文献

1. 唐，彭，鲍德温，曼，江，里斯，卢德克。（2007）eman2：一个可扩展的电子显微镜图像处理套件。结构生物学杂志。157，38-46。PMID:16859925