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Copy path0_vmd_learning.cpp
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45 lines (31 loc) · 1.46 KB
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= reset view
// ##### coloring method #####
ResType: non-polar white, basic blue, acidic red, polar green
Name: O red, N blue, C cyan S yellow
Structure: alpha-purple, beta-yellow, 3-10 helix-blue, turn-cyan, coil-white
// ##### Selections #####
protein, helix,
resname LYS
(not helix) and (not betasheet)
water and (within 3 of helix)
(within 3 of helix) and water
resid 1 4 5 to 9 22
* Extensions->analysis->Sequence viewer
// ref for selection:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.3/ug/node81.html
// ##### Save figures, Rendering #####
Extensions-> visualization->ViewMaster // keep view point
// ##### Creat new material for better representation #####
Graphics->Material // duplicate transparent, and adjust, use white color looks good
// ***** Display->Rendermode->GLSL looks really good. I guess they use render resolution to display.
// ***** orthographic (close look with depth cueing); Perspective (remote view)
// ##### Extensions -> Tk console #####
41 % source vmd_learning_2.vmd
>Main< (vmd) 42 % graphics top text { 40 0 20} "my dear molecule"
// recalculate secondary structure.
vmd_calculate_structure 0 // 0 is molID
// ##############################################
// useful reference:
// ##############################################
1.vmd use program STRIDE ( Frishman et al. Proteins 23:566 1995 to compute the secondary structure according to an heuristic algorithm.