1. 用MS将已经建立好的模型导出为pdb格式的文件
2. 将pdb格式的文件导入到VMD,步骤为file->new molecule..->filename(文件路径)->load
3. 导入的文件在OpenGL Display窗口中显示可能会出现乱七八糟的键,为了清除这些键,在vmd类似于终端的窗口中输入 topo clearbonds,然后回车,这样乱七八糟的键就会没有了
4. 为了重新建立模型中原子间的键,在Graphics->Representations -> Drawing Method(选择DynamicBonds)->Selected Atoms下面空白栏中填入成键关系的原子类型(具体信息在Selections中选择,Selections中keyword中有很多,每一个都有对应的value,双击Keyword中的关键词,Selected Atoms中就会有相对应的显示,也可在Selected atoms 中输入相应的关键词)
5.选择好之后,点击Create Rep就会在(Style Color Selection)下面的空白栏新增一个刚刚操作的新Rep。(注意:创建新Rep的时候,上述额空白栏中之前的Rep不要使选中的状态)
6. 若是更改某一类或者某一些的原子的大小,颜色,则根据上述选择,创建新的Rep进行更改。(此过程若是新的Rep中原子比老的Rep中的Rep原子大,则会覆盖,否则不会覆盖,那就需要删除老的Rep;除此之外,若是通过DynamicBonds建立的键,不会随着新Rep中相对应的成键原子颜色的改变而改变,若想改变通过DynamicBonds建立的键的颜色,则需要通过VMD main窗口中Graphics-> Colors..-->Element中找到相对应的原子种类在Colors中更改颜色,更改之后,OpenGL Display 中通过DynamicBonds 创立的新的键的颜色也就会随之改变。
7. 至于其他原子的颜色大小,键的粗细,都可以在Graphics Representations中进行更改,新的Rep中的参数之后比老的Rep中的参数大时才会覆盖之前的,OpenGL Display中显示的才会有相对应的改变,若是新Rep和老的Rep中的参数相同,虽然OpenGL Display 中也会有相对应的改变,但是如果调整分辨率时,可能会出现新老Rep混合的现象。
8. 至于灯光,VMD main窗口中Display 下有Light 0、Light 1、Light 2、Light 3 四种灯光根据需要选择相对应的灯光(其他不知道),剩下的亮度之类的,应该是在Display--> Display Setting中更改某些参数。
9. 将重新调整好的模型进行输出。
9.1 坐标轴根据需要要不要隐藏,在VMD main --> Display--> Axes 进行坐标轴的显示与关闭
9.2 VMD main --> Display-->Rendermode--GLSL 为了后面使用tachyon渲染器进行输出图片
9.3 模型盒子的显示,若是pdb文件导入的,则在VMD类似终端的窗口输入pbc set {a b c} -all (a、b、c都是对应的在MS中模型实际的数值,单位为Angstrom),其他具体见http://bbs.keinsci.com/thread-3552-1-1.html,也可参考https://www.bilibili.com/read/cv4466929/
9.4 显示模型盒子的框线,则在VMD类似终端的窗口中输入 pbc box -on
9.5 将模型旋转一定的角度,则在VMD类似终端的窗口中输入 rotate x by 90 (此为沿着x轴旋转90度,其他角度根据需要进行更改)
9.6 修改盒子框线颜色粗细,则在VMD类似终端的窗口中输入:pbc box -color red -width 10 -style dashed (该句意思为盒子框线颜色为红色,粗细为10,线型为虚线)参考:http://bbs.keinsci.com/thread-11904-1-1.html
9.7 调整好模型进行输出则是进入File-->Render-->Render the current scene using: Tachyon -->选择保存路径-->Render Command 中输入相对应的参数,具体操作可见https://zhuanlan.zhihu.com/p/398515892;http://bbs.keinsci.com/thread-9178-1-1.html (做此部之前一定要进行9.2的操作)
附:tachyon渲染器中相关Render command 相关参数
Model file formats supported:
filename.dat -- The model files originated with this package.
filaname.ac -- AC3D model files.
filename.nff -- The NFF scene format used by Eric Haines' SPD.
Valid options: (** denotes default behaviour)
----------------------------------------------
Message Options:
+V verbose messages on
-V verbose messages off **
Speed Tuning Options:
-raydepth xxx (maximum ray recursion depth
-numthreads xxx (** default is auto-determined)
-nobounding
-boundthresh xxx (** default threshold is 16)
Shading Options:
-fullshade best quality rendering (and slowest) **
-mediumshade good quality rendering, but no shadows
-lowshade low quality rendering, preview (and fast)
-lowestshade worst quality rendering, preview (and fastest)
Lighting Options:
-rescale_lights xxx rescale light intensity values by
specified factor (performed before other
lighting overrides take effect)
-auto_skylight xxx force use of ambient occlusion lighting,
auto-rescaling direct light sources to
compensate for ambient occlusion factor.
(use value 0.7 as a good starting point)
-add_skylight xxx force use of ambient occlusion lighting,
manually-rescaling direct light sources to
compensate for ambient occlusion factor.
-skylight_samples xxx number of sample rays to shoot.
Specular Highlight Shading Options:
-shade_phong Phong specular highlights
-shade_blinn Blinn's specular highlights**
-shade_blinn_fast fast approximation to Blinn's highlights
-shade_nullphong disable specular highlights
Transparency Shading Options:
-trans_max_surfaces xxx Limit the number of transparent
surfaces shown to the number specified
-trans_orig Original implementation**
-trans_raster3d Raster3D angle-based opacity modulation
-trans_vmd Opacity post-multiply used by VMD
Transparent Surface Shadowing Options:
-shadow_filter_on Transparent objects cast shadows**
-shadow_filter_off Transparent objects do not cast shadows
Fog Shading Options:
-fog_radial Radial fog implementation**
-fog_vmd Planar OpenGL-like fog used by VMD
Surface Normal/Winding Order Fixup Mode:
-normalfixup [off | flip | guess] (**off is default)
Antialiasing Options:
-aasamples xxx (maximum supersamples taken per pixel)
(** default is 0, or scene file determined)
Output Options:
-res Xres Yres override scene-defined output image size
-o outfile.tga set output file name
-clamp clamp pixel values to [0 to 1) (** default)
-normalize normalize pixel values to [0 to 1)
-gamma val normalize apply gamma correction
-format BMP 24-bit Windows BMP (uncompressed)
-format JPEG XXX Not compiled into this binary XXX
-format PNG XXX Not compiled into this binary XXX
-format PPM 24-bit PPM (uncompressed)
-format PPM48 48-bit PPM (uncompressed)
-format PSD48 48-bit PSD (uncompressed)
-format RGB 24-bit SGI RGB (uncompressed)
-format TARGA 24-bit Targa (uncompressed) **
Animation Related Options:
-camfile filename.cam Animate using file of camera positions.
-nosave Disable writing of output frames to disk
(only used for doing real-time rendering)
Interactive Spaceball/SpaceNavigator Control:
-spaceball Enable Spaceball/SpaceNavigator camera flight
-spaceballport serialportdevicename (only for serial devices)