Visualizatin with VMD DAVID CHATFIELD, FIU DEPARTMENT OF CHEMISTRY AND BIOCHEMISTRY WORKSHOP ON MACROMOLECULAR MODELING FIU, APRIL 8-9, 2017 Overview Dwnlad pdb file (experimental structure f macrmlecule) Intr t VMD Manipulating images Saving as an image file fr imprting int anther prgram Tips fr making effective images 1
G t: http://www.rcsb.rg/ Search fr macrmlecule by name, pdb ID, Dwnlad pdb file Type trise phsphate ismerase Click n structure 4ZVJ (human trise phsphate ismmerase) Under Dwnlad Files, chse pdb frmat (NOT the.gz ptin) Save t cnvenient lcatin (e.g. create flder n desktp & save there) Examine pdb file Open file with text editr D NOT try t understand everything Scan fr particular infrmatin, e.g.: Original paper Experimental cnditins Crystallizatin cnditins: 277 K, 35% PEG etc. Missing residues: Gly A - 5, Asp A - 4 etc. Sequence [2 chains: A and B] List f helices and sheets List f x,y,z crdinates Nte: 2 Na +, 2K +, waters at end 2
Dwnlad pdb file (experimental structure f macrmlecule) Intr t VMD Manipulating images Saving as an image file fr imprting int anther prgram Tips fr making effective images Intr t VMD Open VMD 3 Panels appear: Main Display Cmmand (fr typing in cmmands by hand: ignre) 3
Imprt pdb file Main:File: chse New Mlecule In new windw: click Brwse and navigate t pdb file Click Lad: image appears. Play with it using the muse Rtate, zm in and ut (may need t g chse Main:Muse:Scale) Dwnlad pdb file (experimental structure f macrmlecule) Intr t VMD Manipulating images Saving as an image file fr imprting int anther prgram Tips fr making effective images 4
Main:Graphics: chse Representatins Representatins In new windw: Play with Drawing Methd menu (New Ribbns, Cartn, New Cartn, Licrice ) Play with Clring methd (try Element, Chain, Secndary Structure ) Representatins (2) Fcus n ne mnmer (chain): Graphical Representatins: click Create Rep Graphical Representatins:Selected Atms windw: enter chain A (d nt type the qutes) Graphical Representatins: duble click the tp entry in the big windw (it will turn red) Main:Display: click Reset View (image mves t center f display) Graphical Representatins: chse Drawing Methd: New Cartn Clring Methd: Secndary Structure Play arund with the image. Identify the b - barrel. 5
Highlighting a structural element Lp 166-176 is said t frm a hydrgen bnd with the substrate s phsphate. T shw the lp: Create anther representatin Fr Selected Atms, type chain A and resid 166 t 176 Chse Drawing Methd: NewCartn and Clring Methd: ClrID and, just t the right, chse 1 Red Rtate and zm until the lp is clearly visible Dwnlad pdb file (experimental structure f macrmlecule) Intr t VMD Manipulating images Saving as an image file fr imprting int anther prgram Tips fr making effective images 6
Create anther representatin. Make these chices: Selected Atms windw: chain A and resid 95 165 Drawing Methd: Licrice Clring Methd: Element Orient and zm s that His 95 and Glu 165 are large and central, with their relatinship t the TIM barrel clear. Delete the representatin fr lp 166-176. We d nt need it nw. Shw key interatmic distances (angles ) Chse Main:Muse:Label:Bnds Click atm His 95 H bnded t the ring N and the nearest Glu 165 carbxylic O. The interatmic distance (Angstrms) and atm labels shuld appear. Chse Main:Graphics:Labels and delete the atm labels frm the windw. Thse labels just distract; the image is better withut them. 7
Effective image Yu have nw shwn secndary structure (the TIM barrel) with ribbns, key residues atmistically, and an imprtant gemetric parameter quantitatively. This layering f infrmatin at useful levels f detail, using clr wisely, is the key t making effective images. Dwnlad pdb file (experimental structure f macrmlecule) Intr t VMD Manipulating images Saving as an image file fr imprting int anther prgram Tips fr making effective images 8
Imprve the Image fr Exprting First, change the backgrund t white. Black is gd fr the mnitr, but white is almst universally used fr papers, reprts, and presentatins. T d this: Chse Main:Graphics:Clrs. Then in the new windw chse Categries:Display, Names:Backgrund, Clrs: 8 white Imprving Image (2) If the axes are still shwing (depends hw much yu have zmed), remve them: Main:Display:Axes:Off Unless yu really want t shw hw much the riginal crystal structure has been rtated fr this view, the axes are nly a distractin. 9
Imprving Image (3) Ntice that the interatmic distance is n lnger visible (because it is white). T fix: In the Clr Cntrls panel (Main:Graphics:Clrs), chse Categries:Labels, Names:Bnds, Clrs:16 black. T adjust size f distance label, return t the Graphics:Labels windw and chse Bnds in upper left, then Glbal Prperties. Change Text Size and Thickness. Imprving Image (4) Increase the reslutin (therwise edges will appear jagged when image is saved) In Main:Graphics:Representatins, click n the Licrice representatin, and increase the Bnd Reslutin (as high as yu can g and nt create t large a file). Next, click n the NewCartn representatin and increase the reslutin as far as it will g. 10
Nw save the image: Saving an Image File Chse Main:File:Render. Chse Brwse t set lcatin and name f file. Then click Start Rendering. G t the image file s lcatin and click n the file. It is nt yet in a frmat yu can imprtant int a dcument. Yu need t save it in anther frmat. Therefre: Chse File:Exprt. In windw that pps up, chse frmat (e.g. PNG r JPEG). Yu will be able t imprt this int a dcument. Use PyMOL fr even better images fr publicatins & reprts PyMOL Less intuitive (uses scripts) Mre flexibility High reslutin Cumbersme fr understanding research results Great fr publicatin- quality graphics VMD Mre intuitive (pint and click) Less flexibility Mderate reslutin Great fr understanding research results OK fr publicatin- quality graphics 11
Dwnlad pdb file (experimental structure f macrmlecule) Intr t VMD Manipulating images Saving as an image file fr imprting int anther prgram Tips fr making effective images Creating Effective Images Befre yu begin, decide n the pint yu want t make with the image. Let the pint guide yur decisins abut image cmpsitin. Cnsider yur audience early n. What d they need t knw? Cmbine representatins, carefully chsing the level f detail fr each. Use clr, and wisely. Eliminate unnecessary detail: less is ften mre. Every cmpnent f the image shuld have a purpse. 12
Thanks fr yur attentin! Questins? 13