Last week, I posted a blog article that we can make a cube of 3D NMR data but that scripts (at that time) can not draw the labels/axis values. I read the NMRPipe discussion forum today and realized on March 20, the author of NMRPipe has a modified version of nmrCube.tcl and is included in the new version of NMRPipe.
This new nmrCube.tcl now can draw labels as well as the tics/values of each dimension. Here is the example I use my HNCO data to show.
Long time ago, I made a blog article at here to make a record where I can go back to dig information of Ramachandran plot. But the ranges used in the Ramachandran plot are a bit out of date. The Richardson group has a publication in 2003 (Structure validation by Calpha geometry: phi,psi and Cbeta deviation at Proteins) showing a new defined favored and allowed psi/phi ranges.
I learned the defined ranges from a java script provided by an online article by Peter N. Robinson and use the defined values to make an GnuPlot (good for 4.o or above) script to generate my own Ramachandran plot. Robinson’s Java script is easy to make a Ramanchandran plot,too.
Another useful program/tool-kit is the pdb-tools which is currently maintained by Mike Harms and Marcin Cieślik. The pdb-tools provides more than 30 python scripts to dissect, analyze and re-generate the PDB file. I use one of the script “pdb_torsion.py” to generate the psi/phi angles of my calculated proteins.
Now, I have enough tools to get the torsion angles and generate tons of images of Ramachandran plots of calculated proteins automatically. Hooray~.
The result is shown here on the left side. Another figure is generated by MOLMOL in order to provide comparable defined ranges and calculated psi/phi angles.
The ranges I got for Peter N. Robinson’s Java script are posted at here,too.
=== favored (red) regions ====
region 1:
-177.5 -180.0
-177.5 -177.5
-172.5 -177.5
-172.5 -172.5
-167.5 -172.5
-167.5 -167.5
-127.5 -167.5
-127.5 -172.5
-97.5 -172.5
-97.5 -167.5
-77.5 -167.5
-77.5 -172.5
-72.5 -172.5
-72.5 -177.5
-67.5 -177.5
-67.5 -180.0
region 2:
57.5 67.5
57.5 62.5
62.5 62.5
62.5 57.5
67.5 57.5
67.5 47.5
72.5 47.5
77.5 32.5
77.5 2.5
62.5 2.5
62.5 7.5
57.5 7.5
57.5 12.5
52.5 12.5
52.5 22.5
47.5 22.5
47.5 27.5
42.5 27.5
42.5 37.5
37.5 37.5
37.5 62.5
42.5 62.5
42.5 67.5
57.5 67.5
region 3:
-62.5 180.0
-62.5 172.5
-57.5 172.5
-57.5 167.5
-52.5 167.5
-52.5 157.5
-47.5 157.5
-47.5 147.5
-42.5 147.5
-42.5 137.5
-37.5 137.5
-37.5 122.5
-42.5 122.5
-42.5 117.5
-47.5 117.5
-47.5 112.5
-57.5 112.5
-57.5 107.5
-62.5 107.5
-62.5 102.5
-67.5 102.5
-67.5 97.5
-72.5 97.5
-72.5 62.5
-77.5 62.5
-77.5 52.5
-87.5 52.5
-87.5 47.5
-92.5 47.5
-92.5 52.5
-97.5 52.5
-97.5 67.5
-102.5 67.5
-102.5 77.5
-107.5 77.5
-107.5 82.5
-112.5 82.5
-112.5 72.5
-117.5 72.5
-117.5 62.5
-122.5 62.5
-122.5 52.5
-127.5 52.5
-127.5 47.5
-112.5 47.5
-112.5 42.5
-102.5 42.5
-102.5 37.5
-92.5 37.5
-92.5 32.5
-87.5 32.5
-87.5 22.5
-82.5 22.5
-82.5 17.5
-77.5 17.5
-77.5 12.5
-67.5 12.5
-67.5 7.5
-62.5 7.5
-62.5 2.5
-57.5 2.5
-57.5 -7.5
-52.5 -7.5
-52.5 -12.5
-47.5 -12.5
-47.5 -22.5
-42.5 -22.5
-42.5 -32.5
-37.5 -32.5
-37.5 -62.5
-42.5 -62.5
-42.5 -67.5
-77.5 -67.5
-77.5 -62.5
-117.5 -62.5
-117.5 -57.5
-122.5 -57.5
-122.5 -47.5
-127.5 -47.5
-127.5 -37.5
-132.5 -37.5
-132.5 -17.5
-137.5 -17.5
-137.5 2.5
-142.5 2.5
-142.5 32.5
-137.5 32.5
-137.5 52.5
-142.5 52.5
-142.5 57.5
-147.5 57.5
-147.5 67.5
-152.5 67.5
-152.5 77.5
-147.5 77.5
-147.5 87.5
-152.5 87.5
-152.5 97.5
-157.5 97.5
-157.5 112.5
-162.5 112.5
-162.5 122.5
-167.5 122.5
-167.5 132.5
-172.5 132.5
-172.5 142.5
-180.0 142.5
===== allowed (blue) region====
region 1
-180.0 -147.5
-177.5 -147.5
-167.5 -147.5
-167.5 -142.5
-157.5 -142.5
-157.5 -137.5
-147.5 -137.5
-147.5 -132.5
-142.5 -132.5
-142.5 -127.5
-147.5 -127.5
-147.5 -97.5
-152.5 -97.5
-152.5 -92.5
-157.5 -92.5
-157.5 -82.5
-162.5 -82.5
-162.5 -52.5
-157.5 -52.5
-157.5 -37.5
-162.5 -37.5
-162.5 -7.5
-167.5 -7.5
-167.5 32.5
-172.5 32.5
-172.5 52.5
-177.5 52.5
-177.5 77.5
-180.0 77.5
region 2:
-42.5 180.0
-42.5 172.5
-42.5 172.5
-37.5 172.5
-37.5 167.5
-32.5 167.5
-32.5 157.5
-27.5 157.5
-27.5 147.5
-22.5 147.5
-22.5 127.5
-17.5 127.5
-17.5 112.5
-22.5 112.5
-22.5 107.5
-27.5 107.5
-27.5 102.5
-32.5 102.5
-32.5 97.5
-47.5 97.5
-47.5 92.5
-52.5 92.5
-52.5 72.5
-57.5 72.5
-57.5 42.5
-62.5 42.5
-62.5 27.5
-57.5 27.5
-57.5 22.5
-52.5 22.5
-52.5 12.5
-47.5 12.5
-47.5 7.5
-42.5 7.5
-42.5 2.5
-37.5 2.5
-37.5 -7.5
-32.5 -7.5
-32.5 -12.5
-27.5 -12.5
-27.5 -27.5
-22.5 -27.5
-22.5 -47.5
-17.5 -47.5
-17.5 -67.5
-22.5 -67.5
-22.5 -77.5
-27.5 -77.5
-27.5 -82.5
-47.5 -82.5
-47.5 -87.5
-77.5 -87.5
-77.5 -92.5
-87.5 -92.5
-87.5 -112.5
-92.5 -112.5
-92.5 -122.5
-97.5 -122.5
-97.5 -137.5
-92.5 -137.5
-92.5 -142.5
-82.5 -142.5
-82.5 -147.5
-72.5 -147.5
-72.5 -152.5
-67.5 -152.5
-67.5 -157.5
-62.5 -157.5
-62.5 -162.5
-57.5 -162.5
-57.5 -167.5
-52.5 -167.5
-52.5 -172.5
-47.5 -172.5
-47.5 -177.5
-42.5 -177.5
-42.5 -180.0
region 3:
82.5 57.5
87.5 57.5
87.5 42.5
92.5 42.5
92.5 22.5
97.5 22.5
97.5 -17.5
92.5 -17.5
92.5 -22.5
87.5 -22.5
87.5 -27.5
82.5 -27.5
82.5 -37.5
87.5 -37.5
87.5 -47.5
92.5 -47.5
92.5 -57.5
87.5 -57.5
87.5 -67.5
82.5 -67.5
82.5 -72.5
77.5 -72.5
77.5 -77.5
62.5 -77.5
62.5 -72.5
57.5 -72.5
57.5 -67.5
52.5 -67.5
52.5 -37.5
57.5 -37.5
57.5 -27.5
62.5 -27.5
62.5 -22.5
57.5 -22.5
57.5 -12.5
52.5 -12.5
52.5 -7.5
47.5 -7.5
47.5 -2.5
42.5 -2.5
42.5 2.5
37.5 2.5
37.5 12.5
32.5 12.5
32.5 22.5
27.5 22.5
27.5 32.5
22.5 32.5
22.5 47.5
17.5 47.5
17.5 67.5
22.5 67.5
22.5 77.5
27.5 77.5
27.5 82.5
32.5 82.5
32.5 87.5
47.5 87.5
47.5 92.5
67.5 92.5
67.5 87.5
72.5 87.5
72.5 82.5
77.5 82.5
77.5 77.5
82.5 77.5
82.5 57.5
region 4:
72.5 -102.5
72.5 -112.5
77.5 -112.5
77.5 -157.5
72.5 -157.5
72.5 -180.0
57.5 -180.0
57.5 -167.5
52.5 -167.5
52.5 -162.5
47.5 -162.5
47.5 -157.5
42.5 -157.5
42.5 -152.5
37.5 -152.5
37.5 -142.5
32.5 -142.5
32.5 -107.5
37.5 -107.5
37.5 -102.5
42.5 -102.5
42.5 -97.5
52.5 -97.5
52.5 -92.5
62.5 -92.5
62.5 -97.5
67.5 -97.5
67.5 -102.5
72.5 -102.5
region 5:
77.5 180.0
77.5 162.5
82.5 162.5
82.5 147.5
72.5 147.5
72.5 157.5
67.5 157.5
67.5 167.5
62.5 167.5
62.5 180.0
region 6:
162.5 180.0
162.5 147.5
167.5 147.5
167.5 132.5
172.5 132.5
172.5 117.5
177.5 117.5
177.5 77.5
180.0 77.5
region 7:
162.5 -180.0
162.5 -177.5
167.5 -177.5
167.5 -167.5
172.5 -167.5
172.5 -157.5
177.5 -157.5
177.5 -147.5
180.0 -147.5
=========== end of defined values in ramachandran plot ==========
The Gnuplot script is posted at here, in case of missing file in my disc.
The torsion angle file is used as “phipsi.txt” in this script.
==== plot.gnu, use /path/gnuplot plot.gnu to run =======
set terminal png
set output “rama.png”
set noautoscale
set xrange [-180:180]
set xtics -180,30,180 out nomirror
set yrange [-180:180]
set ytics -180,30,180 out nomirror
set tic scale 0.8
set xlabel “phi”
set ylabel “psi”
set arrow from 0, -180 to 0, 180 nohead lw 0.3
set arrow from -180, 0 to 180,0 nohead lw 0.3
set pointsize 0.6
unset key
# LINE COLORS, STYLES
# type ‘test’ to see the colors and point types available.
# Differs from x11 to postscript
# lt chooses a particular line type: -1=black 1=red 2=grn 3=blue 4=purple 5=aqua 6=brn 7=orange 8=light-brn
# lt must be specified before pt for colored points
#
plot “region1″ with l lt 1, “region2″ with l lt 1, “region3″ with l lt 1, “region-w1″ with l lt 3, “region-w2″ with l lt 3,
“region-w3″ with l lt 3, “region-w4″ with l lt 3, “region-w5″ with l lt 3,”region-w6″ with l lt 3, “region-w7″ with l lt 3,
“phipsi.txt” lt -1 pt 5
“Bioinformatics.org” hosts a nice GUI-based PDB file editor. The program is written in Java and can run on MS-Win, Linux and Mac OS. Some snapshopts are showing here. I think this is a very friendly program for users who don’t know how to use shell script to change/reset PDB parameters (e.g. chain ID, beginning number of first residue/atom, remove of heavy atom/water..etc..)
========Program information======
Protein Data Bank (PDB) file editor: web address (http://www.bioinformatics.org/pdbeditor/wiki/Main/HomePage)
=============================
Snapshot 1: target protein coordinate is loaded.
Snapshot 2: the editor window, I reset the beginning residue at 30, and the new ChaiInID is “C”
snapshot 3: the result of new coordinate
***NOTE on April 20****
The nmrCube.tcl has been included in the new version of NMRPipe package and it can label axis, tics and tic values now.
New post is available to show to changes.
*************************
On Feb 18th, an user asked whether there are ways to make a 3D cube of NMR data at the NMRPipe discussion group at Yahoo. Frank Delaglio, the author of NMRPipe, provided a very very nice script to generate the cube. The script is pasted in this post and user can copy it, save it (e.g. nmrCube.tcl) and chmod a+x nmrCube.tcl to make it executable.
I have example pictures showing at here using my 15N-edited NOESY-Hsqc spectrum.
The default colors for background and foreground are black and white, respectively. nmrCube.tcl will draw multi-color peaks in the cube based on the 15N frequency. Here is the example:
I modify the script by changing the default colors (shown in red in the script at here) and run the script like this way:
/path/nmrCube.tcl -hi 5.0e+5 -colors red (fix height and color all peaks in red). The cube is then looked like this way:
So far, no ways for labeling axis and rotation.
===== copy the script and save it as nmrCube.tcl to run ==========
#!/bin/sh
# The next line restarts using nmrWish \
exec nmrWish “$0″ — “$@”
set auto_path “[split $env(TCLPATH) :] $auto_path”
set ARGV [concat $argv0 $argv]
set ARGC [llength $ARGV]
if {[info exists env(NMRTXT)]} \
{
set tStr ” ($env(NMRTXT)/rgb.txt).”
} \
else \
{
set tStr “.”
}
if {[flagLoc $ARGV -help]} \
{
puts “Draw a Simple Static 3D Cube Display of NMRPipe-Format 3D Data:”
puts ” -in inName \[ft/test%03d.ft3\] 3D Spectrum to Draw.”
puts ” -hi hi \[1.0e+5\] Contour Height.”
puts “Spectral Orientation for Drawing :”
puts ” -xName xName \[X_AXIS\] Spectral Axis Name for Plot X-Axis.”
puts ” -yName yName \[Y_AXIS\] Spectral Axis Name for Plot Y-Axis.”
puts ” -zName zName \[Z_AXIS\] Spectral Axis Name for Plot Z-Axis.”
puts “Drawing Sizes:”
puts ” -cxSize cxSize \[400\] Plot X-Axis Size, Pixels.”
puts ” -czSize cySize \[400\] Plot Y-Axis Size, Pixels.”
puts ” -czSize czSize \[Auto\] Plot Z-Axis Size, Pixels.”
puts ” -xAdj xAdj \[16\] Window Horizontal Offset, Pixels.”
puts ” -yAdj yAdj \[32\] Window Vertical Offset, Pixels.”
puts “Drawing Colors:”
puts ” -colors cList \[red ...\] List of Colors for Spectral
Drawing.”
puts ” -fgColor fg \[white\] Forground Color (for Box Outlines).”
puts ” -bgColor bg \[black\] Background Color.”
puts “Notes:”
puts ” 1. The graphic produced is a simple stack of fixed-sized 2D”
puts ” plots with a linear offset.”
puts ” 2. Use ‘-colors multi’ for spectral colors selected according”
puts ” to intensity rather than Z-Axis position.”
puts ” 3. See file ‘rgb.txt’ in the NMRPipe ‘nmrtxt’ directory for valid”
puts ” colors$tStr”
exit 0
}
set inName ft/test%03d.ft3
set hi 1.0e+5
set tMargin 40
set bMargin 120
set lMargin 40
set rMargin 120
set cxSize 400
set cySize 400
set czSize Auto
set xAdj 16
set yAdj 32
set bgColor white #was black
set fgColor black # was white
set colorA black # was white
set colorS white # was black
set xName X_AXIS
set yName Y_AXIS
set zName Z_AXIS
set colorList {red orange yellow green blue cyan orchid}
getArgD $ARGV -in inName
getArgD $ARGV -hi hi
getArgD $ARGV -xName xName
getArgD $ARGV -yName yName
getArgD $ARGV -zName zName
getArgD $ARGV -tMargin tMargin
getArgD $ARGV -bMargin bMargin
getArgD $ARGV -rMargin rMargin
getArgD $ARGV -lMargin lMargin
getArgD $ARGV -cxSize cxSize
getArgD $ARGV -cySize cySize
getArgD $ARGV -czSize czSize
getArgD $ARGV -xAdj xAdj
getArgD $ARGV -yAdj yAdj
getArgD $ARGV -bgColor bgColor
getArgD $ARGV -fgColor bgColor
getArgD $ARGV -colorA colorA
getArgD $ARGV -colorS colorS
getListArgD $ARGV -colors colorList
#
#———————————————————-
wm geom . +$xAdj+$yAdj
wm title . $inName
#
# Check input and its number of planes:
set thisName [format $inName 1]
if {![file exists $thisName]} \
{
puts stderr “Error Finding 3D Input $inName”
exit 1
}
set error [rdFDATA $thisName fdata]
if {$error} \
{
puts stderr “Error Reading Header from 3D Input $inName”
exit 1
}
set dimCount [getParmI $fdata FDDIMCOUNT NULL_DIM]
set zSize [getParmI $fdata NDSIZE CUR_ZDIM]
if {$dimCount != 3 || $zSize < 1} \
{
puts stderr “3D Drawing Error: Data is not 3D.”
exit 1
}
#
# Create the graphics area:
if {![strcasecmp $czSize Auto]} {set czSize [expr int(0.25*($cxSize + $cySize))]}
set wxSize [expr $bMargin + $lMargin + $cxSize + $czSize]
set wySize [expr $tMargin + $bMargin + $cySize + $czSize]
canvas .c -width $wxSize -height $wySize -border 0
pack .c -in . -side top -expand 1 -fill both
button .q -text Quit -command exit
pack .q -in . -side top -expand 1 -fill x
update
.c create pixmap 0 0 -width $wxSize -height $wySize -win 1
#
# Draw the planes:
set nC [llength $colorList]
if {!$nC} \
{
set colorList white
set nC 1
}
set cxn [expr 1 + $wxSize - $rMargin]
set cx1 [expr 1 + $cxn - $cxSize]
set cyn $tMargin
set cy1 [expr $cyn + $cySize - 1]
set iz 1
set xOff [expr int(double($czSize)*($zSize - $iz)/($zSize - 1))]
set yOff [expr int(double($czSize)*($zSize - $iz)/($zSize - 1))]
set tx1 [expr $cx1 - $xOff]
set txn [expr $cxn - $xOff]
set ty1 [expr $cy1 + $yOff]
set tyn [expr $cyn + $yOff]
drawRec -win 1 -x 0% 100% -y 0% 100% -fg $bgColor
drawBox -win 1 -x $cx1 $cxn -y $cy1 $cyn -fg $fgColor
drawLine -win 1 -x $tx1 $cx1 -y $ty1 $cy1 -fg $fgColor
drawLine -win 1 -x $txn $cxn -y $ty1 $cy1 -fg $fgColor
for {set iz $zSize} {$iz >= 1} {incr iz -1} \
{
set xOff [expr int(double($czSize)*($zSize - $iz)/($zSize - 1))]
set yOff [expr int(double($czSize)*($zSize - $iz)/($zSize - 1))]
set ic [expr int(double($nC)*($zSize - $iz)/($zSize - 1))]
if {$ic > $nC – 1} {set ic [expr $nC - 1]}
set color [lindex $colorList $ic]
set tx1 [expr $cx1 - $xOff]
set txn [expr $cxn - $xOff]
set ty1 [expr $cy1 + $xOff]
set tyn [expr $cyn + $xOff]
readROI -ndim 2 -roi 1 -in $inName \
-x $xName 0% 100% -y $yName 0% 100% -dz $zName $iz 0
defineCell -win 1 -cell 1 -x $tx1 $txn -y $ty1 $tyn
defineCell -win 1 -cell 1 -x $tx1 $txn -y $ty1 $tyn
drawROI -win 1 -cell 1 -roi 1 -win 1 \
-hi $hi -bg None -fg None -nobox -color1 $color -color2 $color
update
}
drawLine -win 1 -x $tx1 $cx1 -y $tyn $cyn -fg $fgColor
drawLine -win 1 -x $txn $cxn -y $tyn $cyn -fg $fgColor
drawBox -win 1 -x $tx1 $txn -y $ty1 $tyn -fg $fgColor
update
To make electrostatic surface view of protein using PyMOL, two ways are often suggest. One option is using ABPS to generate the electrostatic map. Here is one nice instruction at PyMOLwiki using ABPS. Another option is using Delphi developed by Barry Honig group to generate the electrostatic map of protein.
I am writing a note at here using Delphi to generate electrostatic surface map of proteins in PyMOL as I learned from one online howto.
Here is the example I have using my project protein:
Note:
I found several good online tutorials of making movies using PyMOL and provide the links at here. I should make some examples by my own next time.
My colleagues asked me to know if they can use PyMol to quickly find information of salt bridges in their working proteins. It seems there is no simple pymol script to do such purpose (at least I can’t find it).
I tried writing a shell scripts to extract coordinates from all negative (Glu, Asp) and positive (Lys, Arg) charged residues and calculate the distances to know if there are any salt bridges in the protein. Before I finish that coding work, I found that VMD actually provide such analysis tool! Good job VMD!.
Here is a snapshot and using protein EnvZ (PDB code: 1BXD) as an example. The output of analysis is shown in the terminal window.
Definition of salt bridge can be found at Wikipedia.
VMD can be downloaded at VMD official site.
When I installed PyMol on my iMac using Fink, I found there are some plugins installed already. One of the famous plugin is PDB loader, I believe every one loves it a lot. A new one (at least it’s new to me) is NMR extension written by a Canadian group. Thank you! I’m lovin it so much.
I don’t know if the downloaded PyMol for Linux or MS-Win also has this plugin installed. If you are an NMR user and want to use PyMol as the main molecular viewer, this is a must-have plugin.
When you click the “NMR Extension”, this pop up window is small as shown below:
At toolbar “File” provides ways to load either single or multiple PDBs as I always did in MOLMOL. Very convenient to load structures. Load PDBs by rootname and number range is another good thing I like a lot.
To load multiple PDBs in one time, simply make a list of taget PDB you want in the .nam file and load the file by clicking the “Load button”. You can see PDBs are loaded in your PyMol main window, like mine:
The structures are not superimposed well and we can do it using the pynmr extension.
Click special in the pynmr window and you will see a refreshed window like this:
I always check on the ” Display Backbone Only” to see backbone trace in the pymol window. If you don’t have a preferred range to do pairwise fit, just click “Do Fit” button and you can all molecules in PyMol window move to the best position. Users can also define the atoms to be superimposed. The plugin provides “C O N CA” and “C N CA” options by default.
You can also see the RMSD (average to mean structure) in the message window. I have checked very times using different calculated multiple structures (different proteins) between this pynmr plugin and MOLMOL, the calculated RMSD values are almost same. Differences happen at the second decimal. Here are the results:
You can also have your own define range in the “Residue range” option, e.g. 10-12,23-34,44-55.
THERE IS NO SPACE between the comma and numbers! Another option is use the “Fit” button to ask the program to guess the best range for you. Unlucky to me, I frequently got all PyMol crashed. Since I know what range/residues I want to use for superimpose, I always manually define the range.
Personally, I don’t like to see oxygen shown in this backbone trace. The default color scheme is too colorful to see the trace. So I always make all molecules in gray (or gray30) and hide the backbone oxygens. The picture is much better as shown below:
Two weeks, I found Agilent’s NMR blog to introduce their design, concept and technology. This is a quite new website created by Agilent. Perhaps it is one of the new strategy to interact with most of young NMR users after Agilent acquired Varian in 2009.
The website address is : http://www.spinsights.net/nmr-blog/.
Hope the Agilent scientists can keep sharing innovative and educational information.
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