I have never used VMD, so have no idea how to run this script. Could you point me to some simple examples for learning how to use these scripts? thanks
From a protein PDB file and for a given residue number, I would like to get the indexes of the four atoms related with psi and phi dihedral angles. Are there useful libraries for this?
5 answers
You you can use VMD's tcl scripting to get phi/psi angles. Bellow is a script originally posted here, but with few modifications.
mol new "1abc.pdb" waitfor all
set fp [ open "phi-psi.dat" w ]
set sel [ atomselect $mol "alpha" ]
set n [ molinfo $mol get numframes ]
for {set i 0 } { $i < $n } { incr i } {
$sel frame $i
$sel update
puts $fp "\# frame: $i"
set a [ $sel num ]
for {set j 0 } { $j < $a } { incr j } {
puts $fp "[expr $j + 1] [lindex [$sel get {resname phi psi}] $j]"
}
}
$sel delete
close $fp
exit
you can run the script in two ways: a) load vmd, go to 'extensions' -> 'Tk Console' and then paste in the script
b) if using linux, save the above script into phi-psiscript.tcl; then in the terminal run 'vmd -dispdev text -e phi-psiscript.tcl'. don't forget to change "1abc" to a pdb file of your choice.
great! I will have a look at. thanks
Have you tried SSTRUC part of JOY package:
Here is first few lines of output for PDB ID: 2DXL. It basically generates this complete file for a given protein structure. You can then parse the output file for residues/regions.
Secondary structure calculation program - copyright by David Keith Smith, 1989
2DXL.atm
HYDROLASE MOL_ID: 1; MOL_ID: 1;
Sequence length - 1626
A A K K hydrogen bonding Ooi's
strk chain/ l amino u & S structure bridge dihedral angles donor acceptor donor acceptor N N
num seq.no t acids t S + patterns partners phi psi omega alpha kappa tco to/energy fr/energy to/energy fr/energy 8 14
1 A 1 MET M e 0 0 999.9 123.3 172.5 999.9 999.9 999.9 0 .0 242 -2.1 0 .0 0 .0 9 38
2 A 2 LEU L E E AA - 241 0 -129.1 120.1 -178.7 -174.5 999.9 169.0 0 .0 43 -3.3 0 .0 44 -1.1 11 43
3 A 3 LEU L E E AAb - 240 44 -116.7 133.3 170.7 -151.1 18.7 160.3 240 -3.2 240 -2.6 0 .0 5 -.7 12 57
4 A 4 ALA A E E AAb - 239 45 -98.4 115.0 -174.0 -166.1 22.9 157.6 44 -2.3 46 -2.7 0 .0 6 -.6 13 61
5 A 5 HIS H E E AAb + 238 46 -113.9 111.2 176.0 163.3 15.5 155.4 238 -3.5 238 -2.5 3 -.7 0 .0 12 74
6 A 6 ILE I E E A b - 0 47 -118.5 165.3 -174.2 -171.0 11.8 143.3 46 -3.1 48 -1.7 4 -.6 0 .0 17 78
7 A 7 SER S + 0 0 -152.5 158.5 166.2 24.5 49.7 168.3 0 .0 215 -1.5 0 .0 0 .0 17 76
8 A 8 ASP D + 0 0 54.9 54.3 -179.7 167.0 51.6 28.6 0 .0 216 -.5 0 .0 0 .0 16 78
9 A 9 THR T - 0 0 -69.5 -32.1 175.2 -161.9 22.4 38.4 0 .0 0 .0 0 .0 0 .0 14 79
============== Removed for brevity =======================
I had a look at the website but did not find anything useful related with my problem
I believe that the 'press' R package allows calculation of psi-phi angles from a PDB file
I had a look at the website but did not find anything useful related with my problem
You can easily do this in BioJava as well if it suits you better.
Here's a code example: http://www.biojava.org/docs/api/org/biojava/bio/structure/Structure.html (See 'How can I calculate Phi and Psi angles of AminoAcids?')
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