Low level commands 简单命令 Classification 分类

classes 文件基于k平均相关数分类

classesbycl 应用等价线分类一组具有中心的颗粒

classesbymra 基于一组参量分类颗粒（常用投影）

classesbymra2 基于多组参量分类颗粒，分别显示2个目录项结果。

classesrefs 基于一组常数分类颗粒

clsregen 应用颗粒分类日志产生重复的cls文件用于特殊的重复

startnrclasses 采用一组颗粒图像产生自由的相关分类平均值

basisclsregen.py 由于执行basisrefine使颗粒重复而产生cls文件

Alignment 调节定向

align2d This program will align a set of images to a reference 根据模版比较一组图片

align3d Rotational and translational alignment of 3d models 旋转平移3D 定向

align3dsym This will rotate a 3D model so its symmetric axes are aligned on the

predefined axes 旋转3D模型，根据已经定义的轴调整定向

align3dsymslow This will rotate a 3D model so its symmetric axes are aligned on the predefined axes旋转3D模型，根据已经定义的轴调整定向

cenalignacf This program will center a set of particles using an autocorrelation function 通过自动调节定义颗粒中心。

cenalignint This iteratively centers a set of particles, using only integer shifts to avoid interpolation artifacts. 重复确定颗粒中心，通过整数调整避免假象

classalign2 Aligns a set of images iteratively to generate a class-average. 重复计算一组图像来产生平均值

classalignall This will align the images in all of the cls*img files in the current directory 调整当前目录下的全部图像 （cls*img files）

geodcmp This will determine a set of orthogonal basis images from a set of aligned particles 从一系列定向颗粒中确定直角坐标系得图像

raw2mrc This program will import raw binary data and write a MRC file 引入原始的二进制数据写成MRC文件

svdcmp This will determine a set of orthogonal basis images from a set of aligned particles从一系列定向颗粒中确定直角坐标系得图像

powdcmp This will determine a set of orthogonal basis images from a set of projections Reconstruction 从一系列投影重构中确定直角坐标系得图像

c1startup This program uses cross-common lines to generate a 3D model from a set of projections 通过投影应用等价线方法产生3D model

clean3d This program uses make3diter and proc3d to iteratively make models match class averages 应用make3diter and proc3d命令重复产生匹配的平均值的模型

make3dlowmem This program builds 3D models from a set of class averages using Fourier techniques 通过一组傅立叶变换方法得到的平均类来建立3D models

make3diter Iteratively improves 3D models using real-space methods. 通过实空间方法重复增强3D models

make3diter2 Iteratively improves 3D models using real-space methods. 通过实空间方法重复增强3D models

make3dreal This program builds a 3d model from a set of projections (class averages) using unfiltered back-projection 通过一系列未过滤得背景投影建立3D models

make3dnonorm This program builds 3D models from a set of class averages using Fourier techniques 通过一组傅立叶变换方法得到的平均类来建立3D models

startAny This program will generate a 3D model from a set of class averages, using cross common lines. 通过一组交叉等价线的方法得到的平均类来建立3D models

startcsym This program generates a preliminary 3d model for objects with Cn or Dn symmetry 通过Cn or Dn对称产生初步的3D模型

starticos This program generates a preliminary 3d model for objects with icosahedral symmetry通过二十面体对称产生初步的3D模型

startoct This program generates a preliminary 3d model for objects with octahedral symmetry通过八面体对称产生初步的3D模型

Transformation/Analysis avg3d This program will average a set of aligned 3d images together 聚集以定向的3D图像

cloud This program performs MSA based filtering of a set of particles 基于一组滤躁的颗粒执行MSA

ctfavg Averages a set of 2D images with ctf correction 通过ctf调整平均化2D图像

ctfavg2 Averages a set of 2D images with ctf correction通过ctf调整平均化2D图像

euler This program calculates a cross common lines image between 2 source images 计算两个源文件的等价线

eulerclassrefine This program will try to refine the Euler angles for a set of class-averages using the concept of common-lines 通过一系列等价线平均数值精确Euler角

eulerproj This program reassigns Euler angles to a set of class averages by projection matching 通过一系列由投影匹配获得的类平均值重新确定Euler角

eulerrefine This program is used internally by startAny 由startAny内部调用

fftavg This program reads a set of images, transforms them, and generates and averaged power spectrum 读取图像，转换图像并且产生平均能谱

footprint This program generates a set of rotational and translational invariants for use in classification 产生一组用于分类的旋转和平移的常量

footprint2 This program generates a set of rotational and translational invariants for use in classification 产生一组用于分类的旋转和平移的常量

footprint3 This program generates a set of rotational and translational invariants for use in classification 产生一组用于分类的旋转和平移的常量

footprintr This program generates a set of rotational and translational invariants for use in classification 产生一组用于分类的旋转和平移的常量

fpweight This program assigns weights to the various axes in a footprint file 指派各轴的权重值

msa This performs multivariate statistical analysis on a set of invariants 一组常量的多元统计分析

msa2 This performs multivariate statistical analysis on 2 sets of invariants两组常量的多元统计分析

project3d Generate projections of a 3D model 产生3D模型的投影

ptcltrace Trace how classification of a single particle changes 追踪单颗粒的分类方法

segment3d Split a 3d map into several pieces. 分块3d图

symbest This program searches a large set of particles for those with the best symmetry. 寻找最佳对称颗粒

symsort Sorts a set of images in order of symmetry quality 以对称质量分类图像

tiltseries Aligns a set of images from a tilt series and assigns Eulers 通过一组已定向的颗粒调整一组图像

volume This program calculates the volume/mass of a 3D map 计算3D图的电子密度值

applyctf Applies/corrects CTF to sets of particle images 应用CTF设置颗粒图像

basisfilter This takes an orthogonal basis set as created by svdcmp and uses it to operate on a set of images 应用由svdcmp产生的直角坐标系来处理图像

batchboxer This program is used for offline boxing of micrographs (MRC format ONLY!) 离线批处理照片

circleboxer This program is used for offline boxing of micrographs using circular contrast regions 离线批处理圆形对比区域的照片

classesbybasis This will classify and align a set of particles based on an orthogonal basis as produced by svdcmp or geodcmp 基于svdcmp or geodcmp产生的直角坐标系来分类和调整一组颗粒

fitctf This program estimates CTF parameters in batch. The results should be checked in CTFIT. 估计一组CTF参数

iminfo This program provides basic information about image files 提供图像的基本信息 make3dsirt Misc. 3d image processing 3D图像处理

mx2img This program converts a distance matrix to an MRC image 转换距离矩阵

pdb2mrc This program will generate a 3D electron density map from PDB files 由PDB文件产生3D电子密度图

proc2d This program performs various processing operations on images and sets of images (WARNING: auto normalization removed) 图像的各种操作和设置

proc3d Misc. 3d image processing 3D图像处理

projtree Generates a list of projections used for high speed particle classification 产生一系列用于高速分类的投影

runpar Run a list of programs in parallel on one or several machines 执行一系列并行的命令

snrboxer This program is used for offline boxing of micrographs (MRC format ONLY!) 离线批处理照片

speedtest This program runs a set of speed tests on the current machine. 机器的速度测试

xtalcen This program will take a diffraction pattern, locate the center, remove the beamstop and do a background subtraction 进行衍射模式，定位中心，删除光点和作背景提取

dejavu2pdb This program generates a pdb backbone for dejaVu helices 为dejaVu helices产生pdb骨架

foldhunter.py Python script for quickly running foldhunterP in chimera Python脚本用于快速运行chimera 中的foldhunterP程序

helix.py This program generates a Ca trace of dejaVu helices 追踪dejaVu helices 中的Ca原子

helixhunter.py Python script for quickly running helixhunter in chimera Python脚本用于快速运行chimera 中的寻找螺旋的程序

sheethunter2.py Beta sheet identification 贝它折叠的确定

lstcat.py Generates a 'lst' file from a set of input image stacks 产生'lst' 文件从图像堆栈中

makeboxref.py Generates an optimal set of reference projections from a 3D model for use in automatic particle selection 自动颗粒选择中的优化投影选择参数

procpdb.py This program is for performing simple operations on PDB files 对PDB files的简单处理

sheethunter2.py Beta sheet identification 贝它折叠的确定

Experimental align3dvec Rotational and translational alignment of 3d models via vectorization 通过向量化旋转和平移调整3D模型

alignhuge Determines the rotation and transformation between images in a focal pair 在焦距对照片中确定旋转和平移调整

classalignml Aligns a set of images using maximum likelihood 通过最大似然化调整一系列图像

classesbymra3 An experimental version of classesbymra classesbymra的试验版本

classesbymrafast This is an experimental classification program 实验分类程序

cosec2iv This program converts helices in COSEC secondary structure elements file format to Open Inventor format 转化的COSEC的二级结构成分的文件格式到Open Inventor format

dejavu2iv This program converts helices in DejaVu secondary structure elements file format to Open Inventor format 转化的DejaVu的二级结构成分的文件格式到Open Inventor format

focalpair Merges focal pairs into a single image with partial CTF correction 通过CTF校正合并焦距对照片

foldhunter This program is used to quantitatively fit a subunit/domain into a large structure density map at intermediate resolution. 定量化亚基形成中度分辨率的结构密度图

foldhunterP This program is used to quantitatively fit a subunit/domain into a large structure density map at intermediate resolution. 定量化亚基形成中度分辨率的结构密度图

helixhunter This program is used to locate possible helices in intermediate resolution maps.在中度分辨率密度图中定义可能的螺旋

helixhunter2 This program is used to find possible alpha-helices region in medium resolution (8Angstrom) density map在中度分辨率图的图中定义可能的alpha螺旋

helixhunter2OMP This program is used to find possible alpha-helices region in medium resolution (8Angstrom) density map在中度分辨率图的图中定义可能的alpha螺旋

helixhunter3 This program is used to find possible alpha-helices region in medium resolution (8Angstrom) density map 在中度分辨率图的图中定义可能的alpha螺旋

helixhunterP This program is used to locate possible helices in intermediate resolution maps. Parallelized. 在中度分辨率图的图中定义可能的alpha螺旋（并行化）

iv2cosec This program converts helices in Open Inventor format to COSEC secondary structure elements file format 转化Open Inventor format的螺旋形成的COSEC的格式文件

iv2dejavu This program converts helices in Open Inventor format to DejaVu secondary structure elements file format 转化Open Inventor format的螺旋形成的DejaVu的格式文件

ivFit This program fits the matched paires of helices returned by COSEC 返回符合相应对的COSEC格式

make3dicos This program builds 3D models from a set of particles with icosahedral symmetry 从一系列的二十面体对称的颗粒中建立3D模型

make3dicos2 Do not use this program directly. It is called from make3dicos. 由make3dicos.调用

matrixembed This program will embed a mutual distance matrix generated by the 'matrix' option of classesbymra 产生由classesbymra产生矩阵的共轭矩阵

matrixclass This program will take a distance matrix and a pre-embedded space 距离矩阵的产生

symAxisSearch This program is used to iteratively search for the local rotation symmtry axis 重复寻找本地旋转对称轴

symeval Experimental - not documented yet

basiseotest.py This is the basisrefine equivalent to eotest 基本精确过程

basismultirefine.py This is a highly experimental refinement procedure using a novel alignment/classification procedure 使用新的分类过程来实验精确过程（多线程）

basisrefine.py This is a highly experimental refinement procedure using a novel alignment/classification procedure使用新的分类过程来实验精确过程

classalignhelix.py This program will take helical cls files and make class-averages 采用螺旋的cls files并确定平均值

classesbymradfilt.py This program is a new version of classesbymra using the dfilt option classesbymra的新版本

classeshelix.py This program will align and classify helical segments vs a set of reference projections

classifykmeans.py This program will classify pre-aligned 2D or 3D images 分类2D or 3D images

evalsim3d.py A simple script that generates projections of a map and uses glmatrix to visually make a similarity comparison 产生投影并应用glmatrix矩阵可视化相似的比较

makeinitialmodel.py Interactively allows the user to make an initial model for iterative reconstruction 重复最初模型的重构

masksym.py This will apply the given symmetry to a mask, and optionally extend the mask 应用给定的对称结构作掩模

project3dhelix.py This program will make axial and near-axial projections of 3D volumes 产生轴和近轴的3D投影

sfmerge.py Combines a structure factor from CTFIT with a simulated curve for use in CTF correction 由CTFIT产生的仿真曲线相连