OLEX2使用手册(指令集)-目录

即日起，将不定时更新关于Olex2自带使用手册《OLEX2 MANUAL (COMMANDS)》的翻译版本《OLEX2使用手册(指令集)》，必要的地方会辅以视频说明。其中有些地方原文有出错的地方，在中文翻译中会更改过来。由于本人英语水平有限，有些翻译可能并不到位，请各位读者海涵！

该手册可在Olex2主界面菜单栏Help下拉菜单中查看，有网页版和PDF版，其中网页版：Documentation (HTML) 为Draft: December, 2010；PDF版：Documentation (PDF) 为Draft: October, 2019

PDF版查看视频教程：https://www.bilibili.com/video/BV1z54y1W7ij

本文是对该手册目录的翻译，英文原文如下：

OLEX2 MANUAL (COMMANDS)

Contents

Introduction................................................................................................................ 3

Understanding the Syntax .................................................................................... 3

Selections and mode .............................................................................................. 4

Tables of Olex2 Commands ................................................................................. 4

Changing the Model View .................................................................................... 4

Keyboard Shortcuts ................................................................................................. 6

Fixed/Refined Parameters ..................................................................................... 7

Atom Connectivity Table Manipulation ........................................................... 8

Symmetry Operations .......................................................................................... 11

Disorder Modelling: Constraints and Restraints ........................................ 12

Selection Syntax ..................................................................................................... 17

HKL file Operations .............................................................................................. 19

Customising the Olex2 GUI ................................................................................ 20

Output: Tables, Reports and Images .............................................................. 21

Structure Analysis .................................................................................................. 23

How to...? .................................................................................................................. 26

Disorder Modelling ............................................................................................... 26

Model disorder across symmetry elements ................................................. 26

Same Site Disorder ................................................................................................ 27

Screen Display ........................................................................................................ 27

Atom Labels ............................................................................................................. 27

Using RESI ................................................................................................................ 28

RESI is a powerful ShelXL tool, by which groupings of atoms belonging to the same RESIdue class can be addressed all at once. ....................................................................................................................................... 28

Graphics and Images ............................................................................................ 28

Draw a Helical Chain around a Rod ................................................................ 28

Working with the Maps display ........................................................................ 31

Get a stereo view ................................................................................................... 31

Colour fragments uniformly .............................................................................. 32

Modifying atomic radii ........................................................................................ 33

Enable hardware 3D and antialiasing ............................................................. 33

Customising molecular display ......................................................................... 34

Tables and Reports ............................................................................................... 36

Automated parameter recalculation ............................................................... 36

Automate tables of selected parameters ...................................................... 36

Space Group Operations ..................................................................................... 36

Change P1 space group to P-1 ......................................................................... 36

Change space group settings ........................................................................... 37

Transforming the axes of a triclinic cell ......................................................... 37

Troubleshooting .................................................................................................... 37

Overlay molecules ................................................................................................. 37

Copy naming scheme from one fragment to another ............................. 38

Get esd's on geometric measurements ......................................................... 39

Pack or grow molecule(s) ................................................................................... 39

To control console and graphics visibility...................................................... 41

Select atoms that became 'too small' ............................................................ 41

Use ShelX programs in Olex2 ............................................................................ 41

Change default programs ................................................................................... 42

Fix tooltips problems ............................................................................................ 42

Rotate a group of atoms around a bond ...................................................... 42

Customise GUI toolbar.......................................................................................... 43

Customising Olex2 Shortcuts and main menu bar .................................... 43

Work with idealised and regularised groups and AFIX instructions ....................................................................................................................................... 43

Troubleshooting .................................................................................................... 44

libpng library problem on Linux ....................................................................... 44

Appendix .................................................................................................................. 45

About Versions and Tags .................................................................................... 45

Installing Olex2 ....................................................................................................... 45

Extension Modules ................................................................................................ 46

Installing Extension Modules ............................................................................ 46

Installation from Olex2 (Online)........................................................................ 46

Offline Installation ................................................................................................ 47

Available Modules ................................................................................................. 47

ReportPlus ................................................................................................................ 47

DrawPlus ................................................................................................................... 47

External Programs ................................................................................................. 48

List of external packages used in Olex2 ........................................................ 48

Credits ....................................................................................................................... 48

翻译成中文后，对于标题进行了一点排版，并且由于还未正本翻译完成，因此暂无页码，中文翻译如下：

OLEX2使用手册(指令集)

目录

1. 前言

1.1. 语法理解

1.2 选择和模式

2. Olex2指令集表

2.1. 更改模型视图

2.2. 键盘快捷键

2.3. 固定/精修参数

2.4. 原子连通性表操作

2.5. 对称操作

2.6. 处理无序模型：约束和限制

2.7. 选择语法

2.8. HKL文件操作

2.9. 自定义Olex2图形用户界面(GUI)

2.10. 输出：表格、报告和图像

2.11. 结构分析

3. 如何……？

3.1. 无序模型处理

3.1.1. 处理穿过对称元素的无序模型

3.1.2. 共占位无序

3.2. 屏幕显示

3.2.1. 原子标签

3.3. 使用RESI

3.3.1. RESI是一个强大的ShelXL工具，通过它可以同时处理属于同一RESI类的原子群

3.4. 图形和图像

3.4.1. 绘制一个绕柱螺旋链

3.4.2. 电子密度图的显示

3.4.3. 获取立体视图

3.4.4. 对片段均匀着色

3.4.5. 修改原子半径

3.4.6. 启用硬件3D和图形保真

3.4.7. 自定义分子显示

3.5. 表格和报告

3.5.1. 自动化参数重新计算

3.5.2. 自动化所选参数表

3.6. 空间群操作

3.6.1. 将P1空间群更改为P-1

3.6.2. 更改空间群设置

3.6.3. 转换三斜晶胞的轴

3.7. 故障排除

3.7.1. 叠加分子

3.8. 将命名方案从一个片段复制到另一个片段

3.9. 获取几何测量的估计标准偏差(esd)

3.10. 堆积或生长分子

3.11. 控制操纵台和图形可见性

3.12. 选择变得“太小”的原子

3.13. 使用Olex2中的ShelX程序

3.14. 更改默认程序

3.15. 修复提示信息问题

3.16. 使一个原子集绕一根键旋转

3.17. 自定义GUI工具条

3.18. 自定义Olex2快捷键和主菜单栏

3.19. 用AFIX命令处理理想化和规则化的基团

4. 故障排除

4.1. Linux中的libpng库问题

5. 附录

5.1. 关于版本和标记

5.2. 安装Olex2

6. 扩展模块

6.1. 安装扩展模块

6.1.1. 从Olex2中安装(在线)

6.1.2. 脱机安装

6.2. 可用模块

6.2.1. ReportPlus

6.2.2. DrawPlus

6.3. 外部程序

7.. Olex2中使用的外部程序包列表

8.. 信用