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3.6.1. 將P1空間群更改為P-1(OLEX2使用手冊(cè))

2021-02-25 13:18 作者:DJ_Tokyo  | 我要投稿

原文如下:


Space Group Operations


Change P1 space group to P-1


Identify two atoms related by the center of inversion, select them and type


>> echo ccrd()


to get coordinates of the point between the selected atoms. This will be fractional coordinates of the proposed centre of inversion as 'x,y,z'. The type:


>> push -x -y -z


to move the content of the asymmetric unit so that the centre of inversion now is at (0,0,0). Then type:


>>changesg P-1


to change the space group. Olex2 will try to remove the symmetry related atoms, however if the atoms do not overlap within some value, they have to be removed manually or by typing:


>>fuse?r


command, where?r?is the radius within which atoms of the same type get merged into a single one.


Sometimes the molecule looks 'broken' after this operation and the command 'compaq -a' has to be executed to assemble the molecule.


譯文如下:


3.6. 空間群操作


3.6.1. 將P1空間群更改為P-1


確定兩個(gè)關(guān)于反演中心相關(guān)的原子,選中它們并鍵入:


>>echo ccrd()


得到選定原子中點(diǎn)的坐標(biāo)。這將是假定反演中心的分?jǐn)?shù)坐標(biāo),即“x,y,z”。鍵入:


>>push -x -y -z


移動(dòng)不對(duì)稱(chēng)單元的內(nèi)容使得反演中心的坐標(biāo)為(0,0,0)。然后鍵入:


>>changesg P-1


更改空間群。Olex2將嘗試去除對(duì)稱(chēng)相關(guān)的原子,但若原子未在某些數(shù)值范圍內(nèi)重疊,它們需要手動(dòng)去除或通過(guò)鍵入:


>>fuse?r


指令,其中r為同一類(lèi)型原子合并成單個(gè)原子的半徑。


有時(shí)在此操作后分子看起來(lái)是“碎裂的”,此時(shí)需要用執(zhí)行指令“compaq -a”用于組裝“碎裂的”分子。


公眾號(hào)文章鏈接:

https://mp.weixin.qq.com/s?__biz=MzU0NjkzMTM1MQ==&mid=2247485336&idx=8&sn=1cdd6b2a11ae074141f4f20e346f1fe9&chksm=fb575060cc20d97694a29a6283ac4c03b804e741fd3346e35d866f910302b0515240000dfe45&token=1126004319&lang=zh_CN#rd



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