1、首先通过 Maestro 生成格点的操作，通过找到通道周围螺旋上同一 Z 轴的残基，找到通道的中心

点（目视判断或根据已有的研究文献）的三维坐标。
2、启动 HOLE 程序

PATH=$PATH:/home/ls/hole2/exe（自己的路径）
hole < hole.inp > hole.txt
Hole.inp 文件内容：
! This is an example of how to run hole
! example input file run on Arseniev's gramicidin structure
! note everything preceeded by a "!" is a comment and will be ignored by HOLE
!
! This example run by line:
! hole < example.inp > example.out &
!
! first cards which must be quoted
! note that HOLE is case insensitive (except file names)
coord XXXX.pdb ! Co-ordinates in pdb format
radius /home/ls/hole2/rad/simple.rad ! Use simple AMBER vdw radii
! n.b. can use ~ in hole
cvect 0 0 159.3 ! channel runs approx up Z axis 注*输入 Z 轴坐标
cpoint 147.8 188.6 159.3 ! a point in pore *格点文件的 xyz 坐标
!
! now optional cards
sample 0.25 ! distance between planes
pltout example.qpt ! quanta plot file output
sphpdb example.sph ! pdb format output of hole sphere centre
! (for use in sphqpt program)
endrad 5. ! to avoid having enormous ends
molqpt stick.qpt ! qpt file of the molecule
! (stick plot in one colour)

egrep "mid-|sampled" hole_out.txt > hole_out.tsv

gnumeric hole_out.tsv（ 安装 gnumeric 可以查看散点图，数据之后可以采用 excel 或者
origin 画图）
sph_process -dotden 15 -color hole_out.sph dotsurface.qpt
qpt_conv 这里会让你选择生成的文件格式，选取 R 生成画图的 rasmol.pdb 格式
initial splash message not shown here

This program converts a .qpt file (as produced by hole)

to something else.
Output options
'A' to/from ascii version of original .qpt (can then edit)
'C' A .qpt file in which dots are replaced by 3D crosses
'L' A .qpt file with long lines split into smaller sections
 (useful for proper depth queueing in qplot)
'I' InsightII format
'R' Rasmol format
'S' Sybyl format
'K' to David C. Richardson's kinemage format
'O' for use with O program
'V' to Virtual Reality Markup Language
'D' to VMD format
Enter conversion option character <stop program>: R

ChimeraX 导入 rasmol.pbd 的操作

setattr g display false ***隐藏缺失序列的虚线
hide bonds ***隐藏 rasmol 的 stick
setattr atom radius 0.1 ***改变原子半径
light depthCue true

注：rasmol.pdb 中间的黄线为通道路径，若影响美观，可以在 pdb 文件里删去。