vmd hands on - unamdepa.fquim.unam.mx/proteinas/pue/vmd-hands-on.pdf · vmd hands on rogelio...
Post on 20-Feb-2019
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VMD tiene dos forma de control
● Las formas gráficas que son múltiples yextensibles
● La ventana de TCL/Tk que es un interprete deun lenguaje llamado TCL
● VMD puede llamarse en modo Python yentonces la interfase acepta comandoPython/Tk-inter
load VMD
● Open a terminal, type:– $ vmd
Main Windowand graphicmenu
VMD consolewhere messages aredisplayed (you mayissue commands here)
Graphic displaywindow, forimagerendering inreal time anduser interaction
other window controls:
Tk console:commandscan beissued here
Labels:graphics->labels
File browser:File-> New mol...
materialsgraphics->materials
Representations:graphics->representations
Menus can also be turned on andMenus can also be turned on andoff with:off with:menu xxxxxx onmenu xxxxxx oni.e., i.e., menu main offmenu main offmenu main onmenu main on
use "menu list" to see all possible options...
let us download a PDB filecd “~”mkdir “mypdb”cd “mypdb”menu pdbtool on
Can also be opened with:Extensions -> PDB query
1ude
Click→ →choose “mypdb”folder, click OK
when done, close the window
load the molecule
● Turn on the Tk console
– % mol new “1ude.pdb”
● get more details on the command mol
– mol ⏎● mol● usage: mol <command> [args...] ...
● Get more documentation at:● http://www.ks.uiuc.edu/
Research/vmd/current/ug/ug.html
● You may turn on the File->new molecule browser● All the features you see here are accessible at command line using
different command options
Let us make it look nice...● graphics →colors
● Display→Background→gray
● graphics→representations● selected atoms: protein● coloring method: Secondary...● Drawing method: New cartoon
● resolution ► 50● Material: EdgyShiny
● Create Rep
● coloring method: color chain
● material: transparent
● Thickness: 0.35● Main menu:
Display→orthographic● light 3 √● render mode: GLSL● axes off
More details...● graphics→representations
● |Create Rep|
● selected atoms: "protein and (sidechain or type CA)"
● coloring method: Type
● Drawing method: CPK
● Sphere/Bond resolution ► 90● Material: Goodsell
● |Create Rep|
● selected atoms: "protein and (sidechain or type CA)"
● coloring method: ResType
● Drawing method: Licorice
● Sphere/Bond resolution ► 90● Material: EdgyShiny
● Create one more representation for:
● "water and (within 6.0 of protein) and not (within 4 of protein)"
● using VDW drawing method to resolution 120, with color element.
Now this is nicer!● Orient and label the molecule:Orient and label the molecule:
– click on the OpenGL displayclick on the OpenGL display
– press "=" on the keybordpress "=" on the keybord
– press s on the keybordpress s on the keybord
– get closer to your molecule (fill area)get closer to your molecule (fill area)
– drag the lower down window corner drag the lower down window corner
– press "r" and rotate your moleculepress "r" and rotate your molecule
– press "t" translate your molecule to a nice positionpress "t" translate your molecule to a nice position
– press "1", click on an atompress "1", click on an atom
– press "2", click on two consecutive atomspress "2", click on two consecutive atoms
– press "3", click on three consecutive atomspress "3", click on three consecutive atoms
– press "4", click on 4 consecutive atomspress "4", click on 4 consecutive atoms
–
resize the displayresize the display
Fix the labels● Neat labelsNeat labels
– Graphics Graphics →→ Labels Labels
– Select atoms. Click on the second row and drag downSelect atoms. Click on the second row and drag down
– |Hide||Hide|
– clickclick
● Type on the Tk console:Type on the Tk console:
– label textsize 2 label textsize 2
– label textthickness 2label textthickness 2
● back to graphic labelsback to graphic labels
– select atoms: click on first lineselect atoms: click on first line
– properties tab, format: %a:%r%d,%cproperties tab, format: %a:%r%d,%c
– reorient your molecule to fit your tastereorient your molecule to fit your taste
● Main Manu: File RenderMain Manu: File Render
Now save a hard copy!● Main menu: File → RenderMain menu: File → Render
– Render using...: Tachyon (internal...Render using...: Tachyon (internal...
– add -fullshade -trans_vmd flags toadd -fullshade -trans_vmd flags tocommand linecommand line
– Set page size: display resize 1000 900Set page size: display resize 1000 900
– |Browse...||Browse...| select "mypdb" folder and select "mypdb" folder andwrite a namewrite a name
– click on click on |Start rendering||Start rendering|
● SAVE YOUR VISUALIZATION STATE:SAVE YOUR VISUALIZATION STATE:
● Main menu: File Main menu: File → Save visualization state→ Save visualization state......
– choose mypdb folder, give file namechoose mypdb folder, give file namestate1.vmdstate1.vmd
Now save a hard copy!
#!/bin/bash# next line is a comment in tcl\cd ${0%/*}# next line is a comment in tcl\exec /PATH2VMD/startup.command -e $0
● Close the program (quit)Close the program (quit)
– cd ~/mypdbcd ~/mypdb
– vi "state1.vmd"vi "state1.vmd"
● add the following lines at theadd the following lines at thebeginning:beginning:
Change name>mv state1.vmd. state1.vmd.sh
Give it execution permissions:>chmod -x state1.vmd.sh
and execute it>./state1.vmd.sh BACK ON BUSINESS IN A JIFFY!
EVEN BETTER
● Load Open office
● create a new blank presentation
● (File -> New-> Presentation... |Create|)
● Insert a square
● double click and add a label
● right-click select "interaction" then choose run program
● select "state1.vmd.sh"
● save your file and go to presentation mode
● click on the box
Click me
click me
Warning:You may need to "explain" gnome how to handle your file, because in order to "runit" open office needs to find out that a "TERMINAL" must be opened and theprogram should be handle to the terminal for execution. Depending oh the configuration of your GNOME/KDE graphic desktop, this may ormay not work without the need for additional changes to system configuration.
Run a small script● Downlad "archivos pdb comprimidos"
● extract in a folder
– >ch $HOME/Downloads (may be $HOME/Decargas)
– >mkdir myfiles ; cd myfile
– >tar -xjvf ../many_pdb.tbz● make sure multiload.vmd.sh is executable
– >ls -lh● run it!
– >./multiload.vmd.sh● let us analize this script
– > gedit multiload.vmd.sh
Let us clean and reset
● Tk console:
– foreach mym [molinfo list] {mol delete $mym}● this command will delete all loaded molecules● no questions asked!
● Do not close vmd, open a new terminal:
● Download the file (moodle site): "mdl_2LWC.tgz" into mypdb
– ch ~/mypdb; tar -xzvf mdl_2LWC.tgz
● Go back to the vmd tk window
● Let us load these files together...
Quit vmd (type quit on the console)● In a new terminal:
– cd ~/mypdb/mdl_2LWC
– vmd
● In the Tk console:
– source "state2.vmd"
● Main Menu: Extensions -> analysis-> RMS trajectory tool
– select "all", remove the noh box, select ref:Average, turn on the plot,click on RMSD.
● Main Menu: Extensions -> visualization-> MakeMovie
– Set directory to ~/mypdb/mdl_2LCW, file name to "movie", method toAnimated GIF, compresion settings to 24 film, Renderer to Tachyon(internal) , movie settings to "trajectory rock".
– click on make movie and wait...
– Open your movie with the WEB browser.
Load the files as frames
● Go back to the vmd tk window
● Let us load these files together
– cd ~/mypdb/mdl_2LWC
– mol new
– foreach nfl [glob 2LWC*.pdb] {mol addfile $nfl}
● change the representation to TYPE/CPK/EdgyShiny● add representation SURF/Element/BrownGlass, set method to
Wireframe, probe 1.5● Now save this state to "state2.vmd"
● let us clean again:
– foreach mym [molinfo list] {mol delete $mym}
Load the files individually
● Now let us load the individually (Tk console):
– foreach nfl [glob 2LWC*.pdb] {mol new $nfl -type pdb}
● Add representations for all (Tk console)
– mol selection "all"
– mol representation "Licorice"
– mol color "element"
– mol material "Glass1"
– foreach nml [molinfo list ] {mol delrep 0 $nml; mol addrep $nml }
● you may now save this state as well, as "state3.vmd"
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