VMD中内置的一些commands说明，用于编写tcl脚本

VMD Tcl脚本语言

动画 animate 控制vmd轨迹动画，读写轨迹帧

animate dup [frame frame_number] molID : 复制给定分子的目前帧（默认）并对分子添加新的帧。
animate forward | animate for : 向前播放轨迹
animate reverse | animate rev : 反向播放
animate pause : 暂停播放
animate prev : 前一帧
animate next : 下一帧
animate skip n : 设置播放步长n，即每多少帧播放一次
animate delete all : 删除所有帧
animate speed n : 播放速度n (0-1)
animate style once : 只播放一次
animate style loop : 循环播放
animate style rock : 播放回放循环
animate styles : 返回可以的styles列表
animate goto [start|end] : 返回第一帧或最后一帧
animate goto n : 前往第n帧
animate read filetype filename [beg nb] [end ne] [skip ns] [waitfor nw] [molecule_number] : 为molecule_number读取类型为file_type的filename文件，从第nb帧开始到第ne帧结束，间隔ns帧。返回读取帧数，nw表示在返回之前读取多少帧
animate write filetype filename[beg nb] [end ne] [skip ns] [waitfor nw] [sel selection] [molecule_number] : 输出类型为filetype名为filename的文件。selection定义输出原子
animate delete [beg nb] [end ne] [skip ns] [molecule_number] : 删除molecule_number数据

animate delete beg 1 end 40

atomselect 选择原子

原子选择用于获取分子中原子信息，分为两步。第一步为生成选择(选择语法，分子id，可选帧数)，atomselect实现此步骤，并返回新选择原子的名称。第二步为使用第一步创建的选择原子获取其信息

atomselect list : 返回被选择原子列表
atomselect keywords : 返回原子选择语句中所有可识别关键词
atomselect macro name selection : 在存在的原子集合之外创建新的singleword原子集合。name必须为单个单词并且以非数字字符开始，不包含空格和特殊字符。selection可以为任何有效的原子选择，也可包含其他的macros。你必须确保macros不包含自身。如果没有selection给定，返回macro的给定名称如果没有name给定，返回所有macro的名称列表如果macro存在，将会被替换。特定关键词不能被重新定义(water、protein). 通俗的讲，macro即为定义的类(water, protein.helix,chain...)
atomselect delmacro name : 删除对应名称的macro。
atomselect molecule_id selection_text [frame frame_number] : 创建新的原子集合并返回命名。selection_text为选择语法。

#example
vmd> atomselect top "name CA"
> atomselect0
vmd> atomselect 3 "resid 25" frame last
> atomselect1
vmd> atomselect top "within 5 of resname LYR" frame 23
> atomselect2

创建的原子集合可以使用以下选项：

atomselect0 num : 返回集合中原子数目
atomselect0 list : 返回选择中原子的索引列表
atomselect0 text : 返回原子选择语法
atomselect0 molid : 返回分子id
atomselect0 frame : 返回原子集合所在帧
atomselect0 frame frame : 设定选择的指定帧
atomselect0 delete : 删除对象
atomselect0 global : 将此对象移至全局命名空间。
atomselect0 uplevel level : 将对象移到新层级
atomselect0 get attribute_list : 获取属性，属性值见手册6.5-6.8

atomselect0 set attribute_list values_list : Set the attributes in the attribute list with the values given in the values lists.

# 简称套中套
set sel [atomselect top all]
set mass [$sel get mass]
set xyz [$sel get {x y z}]
$sel set beta 0 # all values are set to zero
$sel set beta $mass # copy mass to beta
# set occupancy to x, mass to y, beta to z
$sel set {occupancy mass beta} $xyz

atomselect0 getbonds : 返回成键列表
atomselect0 setbonds bonslist : 为原子设置成键信息
atomselect0 move 4x4matrix : 使用4x4矩阵转换原子坐标
atomselect0 moveby offset : 偏移所有原子
atomselect0 lmoveby offset_list : 使用列表中的offset移动每个原子
atomselect0 moveto position : 移动所有原子到指定位置 {x y z}
atomselect0 lmovebyto position_list : 使用列表中的位置移动每个原子
atomselect0 writeXXX filename ：将选定原子写入指定的XXX类型文件(pdb, dcd)
1
2
3
set fd [open filename r];
set s [read $fd];
colse $fd
atomselect0 update : 更新原子选择

axes 坐标

坐标(x,y,z)可以在屏幕显示或隐藏

axes locations : 返回坐标
axes location : 获取当前坐标
axes location <off|origin|lowerleft|lowerright|upperleft|upperright> : 坐标位置

color 修改分子颜色或者编辑色尺，所有颜色值均在0-1。
- color categroy name color : 设置对象颜色(由category和color指定)
- color category name : 获取对象颜色
- color scale method <scale_name> : 设置scale类型用于着色
  
  scale_name:
  
  – RGB – Red to green to blue. – BGR – Blue to green to red. – RWB – Red to white to blue. – BWR – Blue to white to red. – RWG – Red to white to green. – GWR – Green to white to red. – GWB – Green to white to blue. – BWG – Blue to white to green. – BlkW – Black to white. – WBlk – White to black.
- color scale midpoint x : 设置中值
- color scale min x : 设置最小值
- color scale max x : 设置最大值
- color change rgb color：重设rgb为默认值
- color change rbg r g b : 设置rgb颜色为r g b
- color restype resname [restype] : Set the residue type for resname to restype.
- color add item category name colorname : Adds colors for the named color category, item name, using the colorname color

colorinfo

colorinfo categories : 返回可获得的categories列表
colorinfo category category : 返回着色列表名
colorinfo num ：返回基础颜色
colorinfo max ：返回可获得的所有颜色
colorinfo colors ：返回命名颜色列表
colorinfo [index|rgb] <name|values> : returns the index or rgb of the given name or color id

colorinfo scale < method | methods | midpoint | min | max > ：返回色尺的信息

# find out what color corresponds to which id:
set i 0
foreach color [colorinfo colors] {
puts "$i $color"
incr i
}
# also get a list of RGB values
set i 0
foreach color [colorinfo colors] {
lassign [colorinfo rgb $color] r g b
puts "$i $color \{$r $g $b\}"
incr i
}

display

修改显示窗口。
- display get < backgroundgradient | eyesep | focallength | height| distance | antialias | depthcue | culling | rendermode | size | stereo | projection | nearclip | farclip | cuestart | cueend | cuedensity | cuemode shadows | ambientocclusion | aoambi-ent | aodirect | dof | dof fnumber | dof focaldist | backgroundgradient >
- display get < rendermodes | stereomodes | projections>
- display antialias <on|off>
- display ambientocclusion < on | off >
- display aoambient value
- display backgroundgradient < on | off >
- display fps <on | off>
- display [height|distance] value : 设置窗口尺寸
- display resetview : 重置窗口
- display resize valueX valueY : 设置窗口尺寸X Y
- display reposition valueX valueY : 设置窗口左上角的位置坐标
- display shadows <off|on> : Turn shadow rendering on or off. This only affects renderers that support control of shadow rendering. It will have no visible effect on the interactive VMD display or on renderers that don’t support it. At present, only the Tachyon and TachyonInternal renderers are capable of controlling the shadow rendering mode
- display update : 强制显示更新
- display update <on|off>
- display update status

draw

draw command [arguments]

proc vmd_draw_arrow {mol start end} {
# an arrow is made of a cylinder and a cone
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
graphics $mol cylinder $start $middle radius 0.15
graphics $mol cone $middle $end radius 0.25
}

proc label_atom {selection_string label_string} {
set sel [atomselect top $selection_string]
if {[$sel num] != 1} {
error "label_atom: ’$selection_string’ must select 1 atom"
}
# get the coordinates of the atom
lassign [$sel get {x y z}] coord
# and draw the text
draw text $coord $label_string
}

exit

Quit VMD
graphics

graphics是低级绘画命令。可以在分子周围画盒子，在两个原子之间画箭头，标签等等。。。

graphics <molid> <cmd>
- graphics molid point {x y z} : 在指定位置画点
- graphics molid line {x y z} {x y z} [width w] [style <solid|dashed>] : 在两点之间画线
- graphics molid cylinder {x1 y1 z1} {x2 y2 z2} [radius r] [resolution n] [filled <yes|no>]
- graphics molid cone {basex basey basez} {tipz tipy tipz} [radius r] [resolution n]
- graphics molid triangle {x1 y1 z1} {x2 y2 z3} {x3 y3 z3}
- graphics molid trinorm {x1 y1 z1} {x2 y2 z3} {x3 y3 z3} {nx1 y1 z1} {nx2 ny2 nz3} {nx3 ny3 nz3}
- graphics molid tricolor {x1 y1 z1} {x2 y2 z3} {x3 y3 z3} {nx1 y1 z1} {nx2 ny2 nz3} {nx3 ny3 nz3} c1 c2 c3
- graphics molid sphere {x y z} [radius r] [resolution n]
- graphics molid text {x y z} “text string” [size s] [thickness t]
- graphics molid color colorid
- graphics molid color name
- graphics molid color trans_name
- graphics molid materials <on|off> : 对象是否会被光源影响
- graphics molid material <name> : 设置材料
- graphics molid delete [id|all] : 删除graphicsid
- graphics molid [replace|exists|info] id
- graphics molid list
gettimestep

获取时间步长 gettimestep <molid> <timestep>
label

开启或关闭Atoms、Bonds、Angles、Dihedral angles的标签
- label list 返回可获得分类的列表
- label list category 返回所选分类的所有标签
- label add category molid1/atomid1 [molid2/atomid2...]
- label [show|hide|delete] category < all | label number >
- label graph category label_number [filename] : 提取所有步长的标签值
- addspring molID1 atomID1 atomID2 k : 添加连接两个原子的弹簧弹性常数k
- label textsize [newsize] : 获取/设置标签文本字号 1.0(default)
- label textthickness [newthickness] : 获取/设置标签文本粗细 1.0(default)
light vmd内置四个光源(0 1 2 3)，用于照亮图形对象。他们是位于无穷远处的点源，因此设置它们的位置会将它们沿一条来自通过给定点的原点

- `light num` : 返回可获光源数
- `light light_number <on|off|status>` : 打开某个光源，返回光源状态
- `light light_number rot <x|y|z> angle` : 旋转光源一定角度
- `light light_number pos` : 返回光源位置
- `light light_number pos default` : 返回默认位置
- `light light_number pos {x y z}` : 设置光源位置

logfile 是否记录vmd操作命令可以source 重新运行
- logfile filename : log to filename
- logfile console : 将操作记录输出到console，可以通过操作学习命令行如何编写
- logfile off : 关闭日志
To write log information to the file ‘off’, use the file name ‘./off’.
material 创建或者修改材料定义
- material list : 返回可用material
- material settings name : 返回选定材料(name)属性列表
  
  列表顺序为：ambient, specular, diffuse, shininess, mirror, opacity
- material add name : 创建新材料
- material add copy name : 创建一个选定材料的副本
- material rename oldname newname
- material change property name value : 修改材料(name)性质(property)为指定值(value)
  
  property:
  
  – ambient – specular – diffuse – shininess – mirror – opacity
- material delete name : 删除指定材料

measure

measure命令提供多种算法分析分子结构。_selection_表示原子选择集(由atomselect命令得到)，_weight_权重可以为：none; atom selection keyword; lists of values; atom. When an atom selection keyword is used, the weights are taken from selection1.

measure avpos selection [first first] [last last] [step step] : 返回选择原子的平均坐标，如果不定义first last step 默认计算所有帧。
measure center selection [weight weight] ：返回使用权重计算的原子几何中心
measure cluster selection [num numclusters] [distfunc flag] [cutoff cutoff] [first first] [last last] [step step] [selupdate bool] [weight weight] : 对给定权重的原子进行聚类分析(分析项由distance给出)。
- _num_关键词决定使用多少聚类(default 5)
- distfunc : rmsd | fitrmsd | rgyrd |
- cutoff : 两帧之间最大距离截断值(default 1)
- weight : mass | radius (default no weighting)
measure contacts cutoff selection1 [selection2] : 寻找selection1中与selection2中距离小于cutoff的且未与之成键的原子。如果selection2不指定，则使用selection1.

返回两个原子索引列表，分别包含1和2的索引
measure dipole selection [-elementary—-debye] [-geocenter—-masscenter—-origincenter] : 根据电荷值和原子位置计算偶极矩向量。默认单位：电荷基本电荷单位; 距离为埃。默认情况下，结果以相同的单位给出 (与使用_-elementary_ 相同），设置 -debye 标志会将输出转换为德拜单位。在累加所有单独电荷之后，如果_selection_有残基电荷，偶极矩向量依赖于电荷分布中心的选择。默认情况下，中心将是选择的几何中心（与使用_-geocenter_标志相同），也可通过 -masscenter 标志选择质心，通过 -origincenter 标志使用初始中心。建议使用 -masscenter，但它取决于为所有原子正确设置的质量值.
measure fit selection1 selection2 [weight weight] [order index list] : 返回4x4转置矩阵
measure gofr selection1 selection2 [delta value] [rmax value] [usepbc boolean] [selupdate boolean] [first first] [last last] [step step] : 计算原子径向对分布
measure hbonds cutoff angle selection1 [selection2] : 寻找所有的氢键。受体/供体距离在cutoff之内，供体、氢、受体形成的角度必须小于设定的angle.只考虑非氢原子。同时给出selection1 2， 1为供体 2为受体。只给出1 所有的原子既为供体又为受体。返回三个列表(供体索引；受体索引；氢原子索引)
measure inverse matrix : 返回给定4x4矩阵的逆矩阵
measure minmax selection : Returns two vectors, the first containing the minimum x, y, and z coordinates of all atoms in selection, and the second containing the corresponding maxima.
measure rgyr selection [weight weights] : 返回原子回转半径
measure rmsd selection1 selection2 [weight weights] : 返回rmsd
meausre rmsf selection [first first] [last last] [step step] : 返回rmsf
measure sasa srad selection [-points varname] [-restrict restrictedsel] [-samples numsamples] : 计算溶剂可及表面积Returns the solvent-accessible surface area of atoms in the selection using the assigned radius for each atom, extending each radius by srad to find the points on a sphere that are exposed to solvent. If the restrictedsel selection is used, only solvent-accessible points near that selection will be considered. The restrict option can be used to prevent internal protein voids or pockets from affecting the surface area results. The points option can be used to see where the area contributions are coming from, and then the restrict flag can be used to eliminate any unwanted contributions after visualizing them. The varname parameter can be used to collect the points which are determined to be solvent-accessible
measure sumweights selection weight weights : 返回权重集合

measure bond atom_list [options] : 返回两个原子之间的距离

options:

molid
frame measue bond {1 2} frame 1
first
last

measure bond {{atomid1 [molid1]} {atomid2 [molid2]} ... } molid <default molid> frame <frame> first <first> last <frame>
# Returns the distance between atoms 3 and 5 of the current frame of the top molecule
measure bond {3 5}
# Returns the distance between atoms 3 and 5 of molecule 1 for all frames
measure bond {3 5} molid 1 frame all
# Returns the distance between atoms 3 of molecule 0 and atom 5 of molecule 1. The value is computed for all frames between the seventh and the last frame of molecule 0
measure bond {3 {5 1}} molid 0 first 7

measure angle atom_list [options] : 返回角度方法同上定义三个原子
measure dihed atom_list [options] : 返回二面角
measure imprp atom_list [options]
measure energy energy_term atom_list [parameters] [options] : 返回能量项(energy_term : bond angle dihed imprp vdw elect). 能量计算基于CHARMM力场 [options]选项和bond命令相同

parameters：
- k 力常数(kcal/mol/A^2)
- x0 键长键角平衡值
- kub Urey-Bradley force constant for angles in kcal/mol/A2.
- s0 Urey-Bradley equilibrium distance for angles in Angstrom
- n dihedral periodicity
- delta dihedral phase shift in degree (usually 0.0 or 180.0).
- rmin1 VDW equilibrium distance for atom 1 in Angstrom
- rmin2 VDW equilibrium distance for atom 2 in Angstrom
- eps1 VDW energy well depth (epsilon) for atom 1 in kcal/mol
- eps2 VDW energy well depth (epsilon) for atom 2 in kcal/mol
- q1 charge for atom 1
- q2 charge for atom 2
- cutoff nonbonded cutoff distance
- switchdist nonbonded switching distance
  
  所有忽略的参数默认值为0
measure surface selection gridsize radius depth : 返回生成表面的原子索引。gridsize 定义搜索空间网格数 radius 网格点半径距离 depth 深度
measure pbc2onc center [frame frame|last] : 计算变换矩阵将周期性盒子坐标转换为正交晶胞的坐标。由于盒子中心不是由 VMD 存储的，所以必须指定它
measure pbcneighbors center cutoff [options]
measure inertia selection [moments] [eigenvals] : Returns the center of mass and the principles axes of inertia for the selected atoms.

measure symmetry selection [plane|I|Cn|Sn [vector]] [tol value] [nobonds] [verbose level] : 评估原子的对称性。 options:

tol 设置算法容忍度。value越小容忍度越小。default 0.1
nobonds 计算结构不考虑键顺序和方向
verbose 控制输出 0 不输出 1(default)在搜索最后给出部分数据 2 给出额外数据 3 4 数据逐渐增多
I 与其猜测选择的对称点群，不如确定选择的中心偏离质量是否代表反转中心。返回值是介于 0 和 1 之间的分数，其中 1 表示完美匹配
plane Instead of guessing the symmetry pointgroup of the selection determine if the plane with the defined by its normal vector is a mirror plane of the selection. The returned value is a score between 0 and 1 where 1 denotes a perfect match.
Cn|Sn : Instead of guessing the symmetry pointgroup of the selection determine if the rotation or rotary reflection axis Cn/Sn with order n defined by vector exists for the selection. E.g., if you want to query wether the Y-axis has a C3 rotational symmetry you specify C3 {0 1 0}. The returned value is a score between 0 and 1 where 1 denotes a perfect match.
imposeinversion: Impose an inversion center on the structure.
imposeplanes { [ ...]}: Impose the planes given by a list of normal vectors on the structure.
imposeaxes|imposerotref { order [ order ...]}: Impose rotary axes or rotary reflections on the structure specified by a list of pairs of a vector and an integer. Each pair defines an axis and its order.

set sel [atomselect top all]
# Determine the symmetry
set result [measure symmetry $sel]
# Create array ’symm’ containing the results
array set symm $result
# Print selected elements of the array
puts $symm(pointgroup)
puts $symm(order)
puts $symm(elements)
puts $symm(axes)
# Set atoms of selection to ideally symmetric coordinates
$sel set {x y z} $symm(ideal)

menu

菜单命令控制或查询GUI 窗口。
- menu list : 返回可获得的menu名称
- menu menu_name [on|off|status|loc|move x y]
- menu_name:
  - color
  - display
  - files
  - graphics
  - labels
  - main
  - material
  - ramaplot
  - rander
  - sve
  - sequence
  - simulation
  - tool
mol/molecule

molecule_number 字符串，用于选择分子

此命令用于构建representation

 - all 
- top 
- active 
- inactive 
- displayed 
- on 
- off 
- fixed 
- free 
- one of the unique integer ID codes assigned tothe molecules when they are loaded (starting with 0)

mol new [filename] [options]
mol addfile <filename> [options] : 从文件创建新分子如果不指定filename，将会创建一个空白分子 options：
- type <type> 指定文件类型
- first <frame>
- last <frame>
- step <frame>
- waitfor <frames>
- volsets <set ids>
- autobonds <on|off> 是否自动成键
- molid
mol load structure_file_type structure_file [coordinate_file_type coordinate_file] : 导入指定文件类型和文件名的分子，如果指定坐标，同时导入
mol urlload <file_type> <URL> : 从url导入分子
pdbload <four_letter_accession_id> : 导入pdb文件
mol list [molecule_number] : 输出每个分子信息
mol color coloring_method : 改变着色方法
mol material material_name: Change the default material setting.
mol representation rep_style: Change the default rendering method setting.
mol selection select_method: Change the default atom selection setting.
mol clipplane center clipplane_id rep_number molecule_number [ vector ]
mol clipplane color clipplane_id rep_number molecule_number [ vector ]
mol clipplane normal clipplane_id rep_number molecule_number [ vector ]
mol clipplane status clipplane_id rep_number molecule_number [ boolean ]

mol modcolor rep_number molecule_number coloring_method ：设置representation的着色方法
mol modmaterial rep_number molecule_number material_name : 修改representation材质
mol modstyle rep_number molecule_number rep_style : 修改representation渲染方式
mol modselect rep_number molecule_number selection : 选择并创建representation
mol addrep molecule_number ：创建一个presentation

mol default category value
mol delrep rep_number molecule_number
mol modrep rep_number molecule_number
mol delete molecule_number: 删除分子
mol active molecule_number: Make molecule(s) active.
mol inactive molecule_number: Make molecule(s) inactive.
mol on molecule_number: Turn molecule(s) on (make drawn).
mol off molecule_number : Turn molecule(s) off (hide).
mol fix molecule_number: Fix molecule(s).
mol free molecule_number: Unfix molecule(s).
mol top molecule_number: Set the top molecule
mol cancel molecule_number ：取消导入轨迹
mol reanalyze molecule_number : 在成键和原子名修改之后重新载入
mol bondsrecalc molecule_number：重新根据距离计算成键
mol ssrecalc molecule_number: 重新计算二级结构
mol rename molecule_number newname: 重命名指定分子
mol repname molecule_number rep_number: 返回rep命名
mol repindex molecule_number name: Return the rep number for the rep with the given name,or -1 if no rep with that name exists in that molecule
mol selupdate rep_number molecule_number [onoff]: Update the selection for the specified rep each time the molecule’s timestep changes. If onoff is not specified, returns the current update state
mol colupdate rep_number molecule_number [onoff]: Update the calculated color for the specified rep each time the molecule’s timestep changes. If onoff is not specified, returns the current update state.
mol drawframes molecule_number rep_number [frame specification]: Draw multiple trajectory frames or coordinate sets simultaneously. This setting allows the user to select one or more ranges of frames to display simultaneously. The frame specification takes one of the following forms now, frame number, start:end, or start:step:end. If the frame specification is not specified, the command returns the currently active frame selection text
mol smoothrep molecule_number rep_number [n]: Get/set the window size for on-the-fly smoothing of trajectories. Instead of drawing the specified rep from the current coordinates, VMD will calculate the average of the coordinates from the n previous and subsequent timesteps. If n is zero then no smoothing is performed. Note that this smoothing does not affect any label measurements, and does not change the values of the coordinates returned by atom selections or written to files; it only affects how the rep is drawn. Smoothing can be especially useful in visualizing rapidly fluctuating molecules or making movies
mol scaleminmax molecule_number rep_number [min max | auto]: Get/set the color scale range for this rep. Normally the color scale is automatically scaled to the minimum and maximum of the corresponding range of data. This command overrides the autoscaled values with the values you specify. Omit the min and max arguments to get the current values. Use “auto” instead of a min and max to rescale the color scale to the maximum range again.
mol showrep molecule_number rep_number [on | off]: Get/set whether the given rep is shown or hidden. Hidden reps cannot be picked and do not show any graphics.
mol volume molecule_number <volumeset_name> <Origin> <a> <b> <c> #a #b #c <Data>: Add a volumetric data set to the current molecule. Origin, a, b, and c are vectors setting the origin and the three cell vectors. #a, #b, and #c are the number of grid points in the respective cell vector directions and finally the data has to be provided as one list with the data following the grid points along the c-axis fastest, then the b-axis and finally the a-axis.

molinfo

molinfo 用于获取分子信息(原子数、文件名、图像选择、可视化矩阵) 每个分子拥有独有的id，导入时自动分配。有一个独特的分子，其命名为top分子，用于决定一些参数(显示中心、动画控制数据。。。)

molinfo list : 返回当前molecule ids
molinfo num : 返回导入分子数
molinfo top : 返回top分子id

molinfo index n : 返回第n个分子的id

molinfo molecule_id get {list of keywords}

molinfo molecule_id set {list of keywords} {list of values}Access and, in some cases, modify information about a given molecule.

	vmd > molinfo top get numatoms
	568
molinfo 0 get {filetype filename}
	pdb /home/dalke/pdb/bpti.pdb
vmd > molinfo 0 get { {rep 0} {color 0} {rep 1} {color 1} }
{VDW 1.000000 8.000000} {ColorID 5} Lines 1.0000 SegName

mouse

修改目前鼠标状态

mouse mode 0: 旋转
mouse mode 1: 平移
mouse mode 2: 缩放
mouse mode 3 N: 旋转灯N

mouse mode 4 N: 选择mode N

  N:
  - 0 查询
  - 1 选择中心
  - 2 选择原子
  - 3 选择键
  - 4 选择键角
  - 5 选择二面角
  - 6 移动原子
  - 7 移动残基
  - 8 移动片段
  - 9 移动分子
  - 10 作用于原子
  - 11 作用于残基
  - 12 作用于片段

mouse callback on/off
mouse rocking on/off 允许或禁止旋转
mouse stoprotation 停止场景旋转

play
play filename
render
渲染并输出图像

render list : 输出可用的渲染模型
render hasaa method : Query whether or not a renderer has controllable antialiasing feature
render aasamples method samples : 查询或设置抗锯齿样本数
render aosamples method samples : 查询或设置环境光遮挡光照样本数
render formats method: 输出渲染器的输出格式和模式
render format method format: 设置渲染器输出格式

render method filename : 使用method渲染全局对象到文件filename

  method：
  - ART
  - Gelato
  - POV3
  - PostScript
  - Radiance
  - Raster3D
  - Rayshade
  - Renderman
  - snapshot
  - STL
  - Tachyon
  - TachyonInternal
  - VRML-1
  - VRML-2
  - Wavefront

render method filename command

rock 以指定速率旋转当前窗口

rock off: 停止rock
rock <x|y|z> by step: 绕给定轴以一定step速率旋转
rock <x|y|z> by step n : 绕给定轴以一定step速率旋转n次

rotate

rotate stop
rotate <x|y|z> by angle
rotate <x|y|z> to angle
rotate <x|y|z> <by|to> angle step

scale

scale by f: f 放缩因子
scale to f

stage

? Position a checkerboard stage on the screen

• stage location < off | origin | bottom | top | left | right | behind >: Set the location. • stage location: Get the current location. • stage locations: Get a list of possible locations. • stage panels n: Set number of panels in stage, up to 30. • stage panels: Get the number of panels in use

translate

平移物体

translate by x y z
translate to x y z

wait&sleep

wait time
sleep time

callback
vmd callback为一些操作返回值

When called	Name	Description
删除分子(molid)	vmd_molecule(molid)	0
创建分子(molid)	vmd_molecule(molid)	1
重命名分子(molid)	vmd_molecule(molid)	2
导入结构	vmd_initialize_structure(molid)	1
导入坐标文件	vmd_trajectory_read(molid)	坐标文件名
当前帧改变	vmd_frame(molid)	新帧
任何命令执行	vmd_logfile	输出运行命令
pick mode选择原子	vmd_pick_atom	返回index
	vmd_pick_mol
绘制label	vmd_graph_level	{labeltype labelid} {labeltype labelid} ...
	vmd_quit	1

暂时无用命令

help 查看一些程序帮助url
imd 控制远程服务器模拟
mdffi
parllel
tool
user
vmdinfo
volmap