I would like to calculate distance between end c-alpha atoms in some peptide sequences, I'm trying to accomplish this task by writing some perl scripts but i'm facing some errors in my script so I would like to know is there any readily available tools/scripts to do this...
My advice is to use some of the popular protein visualization tools, such as VMD, which contains some scripting facilities. With VMD, using the TCL or Python interfaces it provides will be relatively simple to accomplish the task of your interest.
VMD will by far be the easiest thing to do. However if you have a large number of structures on which u want to do this calculation, you can try MATLAB. There is the command: pdbread( ), which directly reads pdb files into a structure and makes life easy. I've used this to analyse 100s of structures through relatively a short code. However if u have to do the calculation on 5-10 sequences, then the time/effort required to do the MATLAB thing might not be worthwhile - the VMD thing is so much easier.
The following is part of my perl script:
===================================
my ( $x1, $x2, $y1, $y2, $z1, $z2, $r);
my ( $TH1, $TH2, $TH3)=(3.0, 5.0, 7.0);
my $Cnt=0;
open IN, "< $PDBFile"
or die " Can't open file : $PDBFile \n ($!)";
my ( $ChainID, $ResName, $ResNo, $Alt, $AtomName);
my ( $CurrChain, $CurrResNo, $CurrResName)=("_", 0, "");
my $flag=0;
while()
{
if(/^ATOM/)
{
($AtomName,$Alt,$ResName,$ChainID,$ResNo,$x1,$y1,$z1)=unpack("x12 A4 A1 A3 x A1 A4 x4 A8 A8 A8",$_);
$ResNo =~ s/ //g;
$AtomName =~ s/ //g;
# here you get all the information about one atom.
# check and save what is useful and do calculation
}
}
You can do most of the complex analysis of protein structural details using the very powerful scripting features of Visual Molecular Dynamics (VMD; http://www.ks.uiuc.edu/Research/vmd/)
You must however learn some basic tcl/tk or phyton to really use all ist power.
I do not know if you need to measure the distance between consecutive Calpha atoms, or from each Calpha to the Calpha of the C-terminal residue. If you clarify this point I may write you an script to do so in the VMD tcl interphase (menu: extensions/Tcl console).
In any case the command to measure atom-atom lengths is:
measure bond {atomid1 [molid1]} {atomid2 [molid2]}
(the square brackets are optional values, in case you hove more than one molecule loaded in memory)
atomid and molid are integers referring to the atom index and the molecule index. You can identify the index of an atom using the mouse query features (menu mouse, check the label/atoms box on), click on the atom and look at the labels window (opens when you select the graphics/labels menu).
There are many more details at:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node136.html
Thank you so much for sharing your valuable information guys, I've finally debugged my Perl script and its working now but I'll try your suggestions also thnx again.....
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