计算分子尺寸的网站
需要用到分子中各元素的XYZ坐标，这个坐标可以从Chem 3D软件中得到（目前其实不是特别确定导出来的是否准确似乎Chem3D绘制的分子尺寸是近似值，基于所使用的分子模型和计算力场），然后将坐标导入后就可以得到分子的模型和尺寸。
但是这个网站的话，导出的图不方便调整放到文章中，论文用的话可以使用下面的方法。
利用Multiwfn和VMD程序计算尺寸并渲染模型
参考文章：
需要软件：
前两个自行去上面的官网下载即可，ChemDraw可以自行想办法
ChemDraw/Chem 3D绘制分子结构
首先在ChemDraw中绘制出分子结构，然后选中分子结构，Ctrl + C复制后打开Chem 3D，Ctrl + V粘贴进去就就可以得到分子原始的2D结构（右侧）、分子的3D模型（中间）和每个分子元素的对应坐标（左侧）。
然后什么都不用动，直接另存为.pdb文件备用。
PS：直接在Chem3D中绘制好像也可以
Mutiwfn计算
打开Mutiwfn程序，注意打开后是命令行界面，需要输入.pdb文件的路径，回车后依次输入：
100 // 主功能100
21 // 输出各种描述体系结构的信息
size // 计算分子尺寸
此时屏幕上会打印出分子尺寸的信息，这部分信息要保存下来。
此时再输入：
2 // 导出包含尺寸信息的.pdb文件，用于VMD绘图
1 // 显示分子的三维影像
下面显示了程序执行过程：
Multiwfn -- A Multifunctional Wavefunction Analyzer
Version 3.8(dev), release date: 2022-Dec-18
Developer: Tian Lu (Beijing Kein Research Center for Natural Sciences)
Below paper ***MUST BE CITED*** if Multiwfn is utilized in your work:
Tian Lu, Feiwu Chen, J. Comput. Chem., 33, 580-592 (2012)
See "How to cite Multiwfn.pdf" in Multiwfn binary package for more information
Multiwfn official website: http://sobereva.com/multiwfn
Multiwfn English forum: http://sobereva.com/wfnbbs
Multiwfn Chinese forum: http://bbs.keinsci.com/wfn
( Number of parallel threads: 4 Current date: 2023-07-04 Time: 13:51:05 )
Input file path, for example E:\Don't_Toy_with_Me,_Miss_Nagatoro\Hayase_Nagatoro.wfn
(Supported: .mwfn/wfn/wfx/fch/molden/31/chg/pdb/xyz/mol/mol2/cif/cub, etc.)
Hint: Press ENTER button directly can select file in a GUI window. To reload the file last time used, simply input the letter "o". Input such as ?miku.fch can open the miku.fch in the same folder as the file last time used.
C:\Users\iniduoH\Documents\ChemDraw\TEA_C4mPy\C4mPy2+.pdb # 输入.pdb文件路径
Please wait...
Totally 46 atoms
Loaded C:\Users\iniduoH\Documents\ChemDraw\TEA_C4mPy\C4mPy2+.pdb successfully!
Formula: H30 C14 N2
Molecule weight: 226.40193 Da
Point group: C1
"q": Exit program gracefully "r": Load a new file
************ Main function menu ************
0 Show molecular structure and view orbitals
1 Output all properties at a point 2 Topology analysis
3 Output and plot specific property in a line
4 Output and plot specific property in a plane
5 Output and plot specific property within a spatial region (calc. grid data)
6 Check & modify wavefunction
7 Population analysis and calculation of atomic charges
8 Orbital composition analysis 9 Bond order analysis
10 Plot total DOS, partial DOS, OPDOS, local DOS and photoelectron spectrum
11 Plot IR/Raman/UV-Vis/ECD/VCD/ROA/NMR spectrum
12 Quantitative analysis of molecular surface
13 Process grid data (No grid data is presented currently)
14 Adaptive natural density partitioning (AdNDP) analysis
15 Fuzzy atomic space analysis
16 Charge decomposition analysis (CDA) and plot orbital interaction diagram
17 Basin analysis 18 Electron excitation analysis
19 Orbital localization analysis 20 Visual study of weak interaction
21 Energy decomposition analysis 22 Conceptual DFT (CDFT) analysis
23 ETS-NOCV analysis 24 (Hyper)polarizability analysis
25 Electron delocalization and aromaticity analyses
100 Other functions (Part 1) 200 Other functions (Part 2)
300 Other functions (Part 3)
100 # 输入100 //主功能
============ Other functions (Part 1) ============
0 Return
1 Draw scatter graph between two functions and generate their cube files
2 Export various files (mwfn/pdb/xyz/wfn/wfx/molden/fch/47/mkl...) or generate input file of quantum chemistry programs
3 Calculate molecular van der Waals Volume
4 Integrate a function in whole space
5 Show overlap integral between alpha and beta orbitals
6 Monitor SCF convergence process of Gaussian
8 Generate Gaussian input file with initial guess from fragment wavefunctions
9 Evaluate interatomic connectivity and atomic coordination number
11 Calculate overlap and centroid distance between two orbitals
12 Biorthogonalization between alpha and beta orbitals
13 Calculate HOMA and Bird aromaticity index
14 Calculate LOLIPOP (LOL Integrated Pi Over Plane)
15 Calculate intermolecular orbital overlap
17 Generate Fock/KS matrix based on orbital energies and coefficients
18 Yoshizawa's electron transport route analysis
19 Generate new wavefunction by combining fragment wavefunctions
20 Calculate Hellmann-Feynman forces
21 Calculate properties based on geometry information for specific atoms
22 Detect pi orbitals, set occupation numbers and calculate pi composition
23 Fit function distribution to atomic value
24 Obtain NICS_ZZ value for non-planar or tilted system
21 # 输入21 //输出各种描述体系结构的信息
Input indices of the atoms for which geometry information will be calculated
e.g. 1,3-6,8,10-11 means the atoms 1,3,4,5,6,8,10,11 will be considered
Press ENTER button directly will analyze the whole system, input "q" will exit
Other commands:
Input "size" will report size information of the whole system
Input "dist" will report contact/distance between two specific fragments
Input "cav" will report diameter of cavity enclosed by specific atoms
Input "ring" will calculate area and perimeter of a specific ring
Input "MPP" will calculate molecular planarity parameter (MPP) and span of deviation from plane (SDP) for a fragment
size # 输入size //计算分子尺寸，下面六行输出分子尺寸信息
Farthest distance: 17(H ) --- 29(H ): 11.311 Angstrom
vdW radius of 17(H ): 1.200 Angstrom
vdW radius of 29(H ): 1.200 Angstrom
Diameter of the system: 13.711 Angstrom
Radius of the system: 6.856 Angstrom
Length of the three sides: 7.171 7.736 13.575 Angstrom
0 Return
1 Visualize the new orientation and molecular box
2 Export the geometry in new orientation as new.pdb in current folder
1 # 输入1可以显示分子的三维影像
0 Return
1 Visualize the new orientation and molecular box
2 Export the geometry in new orientation as new.pdb in current folder
2 # 输入2可以导出一个记录分子尺寸的.pdb文件，该文件用于在VMD程序中绘图
Exporting new.pdb file finished!
0 Return
1 Visualize the new orientation and molecular box
2 Export the geometry in new orientation as new.pdb in current folder
VMD绘制
用VMD程序打开上一步中使用Mutiwfn导出的新的.pdb文件（可以直接将文件拖到VMD的主窗口中），然后在命令行窗口中输入pbc box，盒子就显示出来了。
接下来就要修改一些VMD的显示参数：
将分子结构显示为球棍模型：菜单栏打开Graphics-Presentations，将Drawing Method改为CPK。
更改背景颜色：菜单栏打开Graphics-Colors，选择Display-Background，修改为White。
更改元素颜色：同样打开菜单栏的Graphics-Colors，选择Name，将对应的元素设置为自己想要的颜色。
选择正交视角：菜单栏选择Display，选择Orthographic。
删除左下角坐标轴：菜单栏选择Display-Axes，选择Off选项。
渲染：完成上一步直接导出图片的话分辨率比较低，所以需要重新渲染。首先菜单栏打开File-Render，在第一栏Render the current scene using：选择Tachyon，下面的Filename默认为
vmdscene.dat，Render Command默认为"C:\Program Files (x86)\University of Illinois\VMD\\tachyon_WIN32.exe" -aasamples 12 %s -format BMP -o %s.bmp，可以点击Filename右侧的Browse看一下vmdscene.dat的保存路径，然后Start Rendering，就会在刚刚Browse的目录下生成vmdscene.dat文件（实际情况发现并没有生成在该目录下，具体位置可以使用Everything程序查找一下），这时需要在这个目录下复制两个文件进去（文件会放在文章的最后）：tachyon_WIN32.exe和render.bat，然后运行这个批处理脚本，就可以得到清晰度比较高的.bmp文件，可以放在论文中使用。
最后可以在分子模型图中P上使用Multiwfn计算得到的长宽高即完成。