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olex2初级指南
Olex2 初级指南
By lich666（email ：，qq ：） 0 前言
0.1 为什么要使用olex2
Olex2同shelxtl 类似，均为集成的晶体解析软件，具有解析、精修、画图等多种功能。二者均是年龄10年以上的老软件了，许多晶体学软件已经不更新了，但是它们依然有人维护，不断推出新版本。随着不断发展，二者已臻成熟，不乏使用者。经过本人使用，发现两者有诸多优缺点。
Olex2具有美观的图形界面，可以用鼠标操作，使用方便快捷。而shelxtl 大多数时候只有一个黑洞洞的屏幕，且需要使用键盘输入命令，略繁琐。
Olex2具有方便的数据回滚功能，当进行多次尝试时可以直接回滚，无需手动保存
Olex2扩展性强，可以方便调用多种解析和精修软件，而且可以直接调用platon 。Shelxtl 只能使用自带的xs 和xl 软件。
Olex2 虽然自带多种实用工具，如solvent mask 和twinning 等，但是这些工具多半有瑕疵，发文章不推荐使用，去除溶剂和孪晶最好用platon 代替。Shelxtl 所带的工具较少，仅有Xprep ，但可以帮我们解决许多问题。
Olex2具有上述多种优点，下面就开始olex2从头开始的教程。
本教程只是给自己实验室留点纪念且想给学习olex2的同学们一个参考，文中仅代表个人观点，本人学习结构解析仅两年有余，olex2软件全靠自己钻研，难免有疏漏，如有错误请直接指出。
0.2 配置olex2
首先需要到网站（这个网站现在需要注册）上下载olex2的最新版本1.2.5，推荐下载绿色版本，直接解压缩就可以使用，且32位系统下载32位版本，64位版本下载64位版本（本教程以64位版本为例，如果懒得去官网可去百度网盘下载已按下文配置好的版本，百度网盘里还有platon 和shelx2013中的shelxl 、shelxs ）。然后将压缩包解压，放置在一个没有中文路径名的文件夹里，如D:\c\olex2-win64中。
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&&【交流】Olex2 教程
【交流】Olex2 教程
Olex2 Manual
Draft: June, 2010
1. Introduction ........................................................................................................ 1
2. Understanding the Syntax .................................................................................... 2
3. Tables of Olex2 Commands .................................................................................. 3
Changing the Model View .......................................................................................................... 3
Keyboard Shortcuts.................................................................................................................... 4
Fixed/Refined Parameters......................................................................................................... 5
Atom Connectivity Table Manipulation .................................................................................... 6
Symmetry Operations ................................................................................................................ 7
Disorder Modelling: Constraints and Restraints ...................................................................... 9
Selection Syntax ........................................................................................................................12
HKL file Operations ..................................................................................................................12
Customising the Olex2 GUI ......................................................................................................13
Output: Tables, Reports and Images........................................................................................14
Structure Analysis ..................................................................................................................... 15
4. Appendix.............................................................................................................17
About Versions and Tags .......................................................................................................... 17
Installing Olex2.........................................................................................................................18
Windows:..............................................................................................................................18
External Progams......................................................................................................................18
SHELX ..................................................................................................................................18
Platon....................................................................................................................................19
SuperFlip ...............................................................................................................................19
About Macros and Scripting in Olex2.......................................................................................19
This document describes some of the commands that are available in Olex2. Many of these
commands are also available directly from the Olex2 Graphical User Interface. Most is on the
GUI have a small 'info' symbol next to them, where you can find out more about any of these is.
1. Introduction
There is no special console window in Olex2 -the commands described in this document can
be typed where ever you are in Olex2 and the text you type (as well as the program response) will
appear in the bottom left hand corner of the main window. The text will then scroll up behind
the displayed molecule. The number of lines of text that are visible can be set with the command
lines n. You can also toggle ween showing the molecule only, showing the text only and
showing both at the same time (default) using CTR+T. You can always examine the text output in
your default text editor by typing text.
Many commands in Olex2 are modelled on the syntax that may be familiar from SHELX: four
letter commands, where the letters often provide a hint about the function of the command. Many
commands that are available in ShelXP, for example, can be used in Olex2. Also, all commands of
the ShelXL and ShelXS syntax are interpreted by Olex2 and used to construct the internal Olex2
structure model. This model is then used directly to carry out a smtbx-refine refinement, whereas
a shelx.ins file is generated on the fly if ShelXL/XH is chosen for the refinement.
All commands in Olex2 will auto-complete when pressing the TAB key. If the completion
is not possible, because there is more than one command starting with the letters that have been
typed, a list of these commands will be printed. It is good practice to use the auto-complete
2. Understanding the Syntax
Selection: If one or more atoms are selected on the screen, then any command that acts on a selection
will apply to the selected atoms only. If there is no selection, it will apply to all atoms. Instead of
making a selection on the screen, a list of atom names can also be supplied. If a command has been
successful, the selection will disappear. (Although there are a couple of exceptions to this rule)
Mode: If Olex2 is in a Mode, the chosen action will be applied to all subsequently clicked atoms. The mouse
pointer will change from the default arrow symbol to signify that Olex2 is in a mode. To get out of a mode,
simply press the ESC key.
Syntax used in this document:
{a, b, c}: choice of a, b or c. For example: fix {occu, xyz, Uiso}&&means 'fix occu ', 'fix xyz
', 'fix Uiso '.
: optional parameter. This parameter is not required for the command to work, and if it is not supplied,
the default value will be used.
-k: This is an option switch.
i: Italic characters are used for variables.
means an optional list of atoms. Any atoms that are selected will automatically be present in this list.
If there are no selected atoms, all atoms will be in this list. Alternatively, the atom names of the atoms that
should appear in this list can be typed by hand.
atoms means a compulsory list of atoms. Any atoms that are selected will automatically be present in this list.
Alternatively, the atom names of the atoms that should appear in this list can be typed by hand.
Capital Letters are used for commands that will directly affect the structure model in the refinement. These
commands will become part of the structure model and will appear in the ShelX input file. Please note that
these commands can be typed either in upper or lower case.
Example Commands are resented in this format: refine 4 20 and can be typed exactly as they are given.
In this example, the structure will be refined with 4 refinement cycles and 20 electron density peaks will be
returned from the electron density map integration.
3. Tables of Olex2 Commands
3. 1 Changing the Model View
matr&&or&&or
Orients the model along a (1 or 100), b (2 or 010), c (3 or
001) or any other crystallographic direction, like 123, which
sets current normal along (1*a+2*b+3*c) vector. Two
crystallographic directions (from and to) may be specified
align current view normal along the (to-from) vector. Also a
full Cartesian matrix can be specified. If the directions are
signed or consist of multiple digits all components should be
of the same length like in 120101 or -1+1+1 (same as -10101).
If no arguments given, prints current Cartesian orientation
. matr 1 or matr a or matr 100 - sets current normal
along the crystallographic a direction
. matr 100 011 sets current normal along (011-100)
direction (the normal direction changes if from and to are
rota&&or&&
Changes current view by rotating around given axis (x, y or z)
when two arguments are provided and makes a continuous
rotation around give axis when 5 arguments are provided.
Note that X axis is aligned horizontally, Y - vertically and Z is
out of the screen plane.
. rota x 90 rotates the structure 90 degrees around X axis
. rota 0 0 1 90 1 rotates model in the screen plane
(around Z) 90 degrees with 1 degree increment.
direction The command prints current normal in crystallographic
coordinates and tries to match it to a crystallographic
direction.
Finds the best plane through the current selection or given
atoms, or out of all visible atoms if none are given.
. -n sets the view along the normal of the plane
. -r: creates a regular plane
. rota x 90 rotates the structure 90 degrees around X axis
. rota 0 0 1 90 1 rotates model in the screen plane
(around Z) 90 degrees with 1 degree increment.
direction The command prints current normal in crystallographic
coordinates and tries to match it to a crystallographic
direction.
Finds the best plane through the current selection or given
atoms, or out of all visible atoms if none are given.
. -n sets the view along the normal of the plane
. -r: creates a regular plane
The model can be rotated using by moving the mouse pointer while holding the left mouse button down (also
Shift+arrow keys); rotated around Z by pressing the CTRL key zoomed using the right
mouse button (also Shift+Home/End). The default mouse behaviour can be overridden in some modes (look at
mode split) also some objects, like cell basis or text boxes can override some mouse operations (like zooming
on the cell basis) or extend it (moving the basis while holding Shift key down).
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扫描下载送金币主题培训通知1.&&培训标题&&晶体结构解析-理论与实践2.&&主题背景和培训必要性&&晶体学博大精深，晶体材料应用也很广阔。晶体结构解析是晶体学与材料相关学科研究中的一项重要基本任务。近年来，随着晶体结构理论和相关计算机程序的发展，在以材料功能为导向的结构研究背景下，材料深层次结构信息的提取变得十分重要。&&&&Shelxtl是目前解析单晶结构的常用软件包之一，其历史悠久，功能强大，但也较为固化，比较适合于常规结构解析。近年来出现了比直接法(被Shelxtl采用)更有效的晶体结构解析算法和采用此算法的结构解析软件，其中具有代表性的是Charge flipping算法和Jana软件。实际测试表明，对于一些较差的单晶衍射数据，Jana能给出比Shelxtl更准确的初始结构，且Jana在特殊调制结构(modulated structure)解析、无序结构和高阶精修等诸多方面具有更完善和更强大的功能，因此Jana更适合于非常规结构的解析，这也比较符合目前材料研究中对精细结构调控的研究需求。Olex软件则集成了Shelxltl和Jana等若干晶体结构解析子程序，便于用户自由调用。&&&&Fullprof是一款专业的粉末结构解析和精修的软件，对于无法测得单晶衍射数据，只有粉末衍射数据的情况下，Fullprof能对粉末XRD谱进行指标化并通过模拟退火算法得到单晶结构。Fullprof拥有的粉末结构解析与精修功能对于纳米、粉体、多晶等许多材料领域的研究都十分重要。&&系统性的掌握Shelxtl和Jana解析材料单晶结构，以及Fullprof解析和精修粉末结构的方法，无论对于晶体学初学者，还是晶体学、材料物理化学等相关领域的研究人员都很有必要。3.&&培训主要内容1）&&全面系统的讲解晶体学基础（点阵与对称元素、等效点系、点群与空间群等）；晶体物理学基础（群论基础、对称性与物理性质的关系、物性张量、不可约表示、子群与相变等）；X-ray衍射基础（倒空间、傅里叶变换、衍射几何与结构因子、消光规律、取向矩阵等）、结构解析理论基础（直接法、charge flipping法、最小二乘精修等）、重要晶体学专著International Tables for Crystallography (Volume A)&和网站资源Bilbao Crystallographic Server的使用方法。2）&&通过全面系统的实例讲解和实践训练，掌握Shelxtl, Jana, Olex解单晶结构和Fullprof粉末法解结构的方法，了解Shelxtl特别是Jana对双晶，非公度和四维调制结构等特殊结构的解析、无序处理与温度因子高阶精修方法。4.&&与本培训有关的学科和研究领域&&晶体学、材料、物理、化学学科中凡与材料晶体结构有关的研究领域5. &培训专家介绍&&姜小明：中科院福建物质结构研究所无机化学博士，南京大学凝聚态物理博士后，德国慕尼黑工业大学无机化学博士后，在晶体结构与磁结构，非线性光学、铁电、多铁与磁学性能等方面有多年的研究经历，有较强的晶体学理论功底和多年的晶体结构和磁结构分析软件的编程经历。6.&&培训日程表注：1）&&考虑到学员可能具有不同的研究方向和基础，实际培训的具体内容可能有少许变动。2）&&学员需自带笔记本电脑。第一天晶体学理论8:30-9:00学员注册报到，领取培训资料9:00-9:30学员自我介绍9:30-10:30讲解晶体学基础：点阵与对称元素、等效点系、布拉维（Bravais）格子、点群与空间群10:30-10:45茶歇与讨论10:45-12:00讲解晶体物理学基础：群论基础、对称性与物理性质的关系、物性张量、不可约表示、子群与相变&&12:00-14:00午餐14:00-15:00讲解X-ray衍射基础：倒空间、傅里叶变换、衍射几何与结构因子、消光规律、取向矩阵、衍射点指标化与强度积分15:00-15:15茶歇与讨论15:15-16:15讲解结构解析理论基础：直接法、charge flipping法、最小二乘精修16:15-16:30茶歇与讨论16:30-17:30讲解重要晶体学专著International Tables for Crystallography (Volume A)&和网站资源bilbao crystallographic server的使用方法17:30-18:00茶歇与讨论第二天Shelxtl8:30-9:30讲解Shelxtl各模块使用方法：XPREP, XS, & XL, XP, XCIF9:30-10:00茶歇与讨论10:00-12:00实例讲解与实践训练，掌握Shelxtl单晶结构解析的基本方法和通用流程12:00-14:00午餐14:00-15:00讲解特殊结构的处理方法：Platon使用方法、双晶和无序结构的处理、格子人工转换15:00-15:30茶歇与讨论15:30-18:00实例讲解与实践训练，掌握双晶、无序结构、不良原始数据的处理方法、结构精修技巧第三天Jana8:30-10:00讲解Jana各模块使用方法：EditM50, Edit atoms, Edit profile, Structure solution, Refine等10:00-10:30茶歇与讨论10:30-12:00实例讲解与实践训练，掌握Jana单晶结构解析的基本方法和通用流程12:00-14:00午餐14:00-15:00讲解特殊结构理论：双晶，非公度和四维调制结构（modulated structures）解析、无序与温度因子高阶精修15:00-15:30茶歇与讨论15:30-18:00实例讲解与实践训练，掌握双晶，非公度和四维调制结构的处理、无序与温度因子的高阶精修第四天Olex和Fullprof8:30-9:30讲解Olex使用方法，Olex解结构基本流程9:30-10:00茶歇与讨论10:00-11:30讲解Fullprof程序和各模块的使用：WinPlotr, & Edit PCR等11:30-12:00茶歇与讨论12:00-14:00午餐14:00-15:00实例讲解与实践训练：掌握Fullprof的基本操作、粉末XRD峰的指标化、Retiveld精修15:00-15:30茶歇与讨论15:30-18:00实例讲解与实践训练：粉末XRD法解结构(针对问题：对于只知道大致结构模型和构筑单元，但没有单晶衍射数据的化合物，如何通过粉末XRD谱的模拟退火算法得到单晶结构)培训结束&7.&&培训时间/地点时间：2017年1月16-19日（四整天）地点：福州市，中科院福建物质结构研究所(详细地点见邮件通知)8.&&培训费用RMB 5000 (包括培训费、午餐费，不包含差旅及住宿费)，限28人；报名费可现场支付，若2017年1月6日前付款则只需支付RMB 4600。9.&&汇款账户账户名：福州水草云信息咨询有限公司账户：1062247开户行：中国工商银行福州洪山支行10.&&报名参加填写报名表(可在网站上‘报名参加’链接中下载)，并发送到邮箱：或通过网站提交报名：&11.&&联系方式Mobile: 赵女士Email:&&水草云团队2016年10月6日
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&&请问大家，win10怎么安装shelxtl
请问大家，win10怎么安装shelxtl
前段时间电脑更新到win10，shelxtl正常使用，但是手贱嫌电脑卡，又重新装了一个win10专业版的，shelxtl就用不了了。。求大神怎么破？？
注：之前LZ电脑win7的，用“64位win7 装SHELXTL的方法”装上的。
按照上面的操作就好 了，
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