原文如下：

Get esd's on geometric measurements

Olex2 can calculate esd's on a variety of geometric measurements, also if a CIF is loaded into Olex2 then esd's available in the CIF (bond lengths and the angles) will be displayed in the tooltip when hovering over the bonds or selection of the bonds; use the 'sel' command to print the values in the console.

To calculate the esd's Olex2 need the variance-covariance matrix. This can be readily produced by shelxl when refining with a negative MORE instruction (like MORE -1). It also will be soon available from the smtbx refinement. Once the matrix file is available, the geometric parameters can be easily calculated by selecting:

a bond or two atoms – length two bonds or three atoms – angle four atoms - torsion angle and the tetrahedron volume a plane - RMSD and the centroid coordinates in fractional and Cartesian coordinates a plane and an atom - atom to plane and atom to plane centroid distances a plane and a bond - angle between the plane normal and the bond two planes - angle between the plane normals, plane centroid to plane centroid, plane to centroid and the shift between the plane centroids distances three planes - the angle between the plane centroids

Then type:

>>esd

to get the measurements with esd's.

Note that the current implementation of the esd calculation procedure does not consider symmetry constraints and gives esd's even for the symmetry related parameters.

譯文如下：

3.9. 獲取幾何測(cè)量的估計(jì)標(biāo)準(zhǔn)偏差(esd)

Olex2可以計(jì)算各種幾何測(cè)量的估計(jì)標(biāo)準(zhǔn)偏差(esd, Estimated Standard Deviation)，若將CIF加載到Olex2中，當(dāng)鼠標(biāo)懸停在鍵或選定鍵上時(shí)，工具提示中將顯示CIF中可用的esd(鍵長(zhǎng)和角度)；使用'sel'指令在控制臺(tái)中打印這些數(shù)值。

為計(jì)算esd，Olex2需要方差-協(xié)方差矩陣。當(dāng)使用負(fù)的MORE指令(如MORE -1)進(jìn)行精修時(shí)，shelxl可很容易地獲得所需方差-協(xié)方差矩陣。它也很快將從smtbx精修中提供。一旦矩陣文件可用，幾何參數(shù)可以很容易地通過(guò)以下選擇進(jìn)行計(jì)算：

一根鍵或兩個(gè)原子——鍵長(zhǎng)(距離)

兩根鍵或三個(gè)原子——鍵角

四個(gè)原子——扭轉(zhuǎn)角和四面體體積

一個(gè)平面——RMSD和質(zhì)心的分?jǐn)?shù)坐標(biāo)和笛卡爾坐標(biāo)

一個(gè)平面和一個(gè)原子——原子到平面距離和原子到平面質(zhì)心距離

一個(gè)平面和一根鍵——平面法線(xiàn)與該鍵夾角

兩個(gè)平面——兩個(gè)平面法線(xiàn)夾角、兩個(gè)平面質(zhì)心間距、平面到質(zhì)心間距以及兩個(gè)平面質(zhì)心滑移間距

三個(gè)平面——三個(gè)平面質(zhì)心形成的夾角

然后鍵入

>>esd

以獲取上述測(cè)量的esd。

請(qǐng)注意，esd計(jì)算程序的當(dāng)前執(zhí)行程序沒(méi)有考慮對(duì)稱(chēng)性，甚至對(duì)對(duì)稱(chēng)性相關(guān)參數(shù)也給出了esd。

本文輔助視頻如下：

Olex2視頻教程——指令sel的應(yīng)用

https://www.bilibili.com/video/BV1ib411u7r2

Olex2視頻教程——指令mpln的使用

https://www.bilibili.com/video/BV1ob411W79i

公眾號(hào)文章鏈接：

https://mp.weixin.qq.com/s?__biz=MzU0NjkzMTM1MQ==&mid=2247485350&idx=4&sn=af36dcb8d79539db2edfa81b15795666&chksm=fb57505ecc20d948eb5601fe97149e122a8152b8c9c10d9e2b64e3bae207dc29e22515b19aa3&token=1126004319&lang=zh_CN#rd