[Biopython] Protein side-chain angles from a PDB file

[Rodrigo faccioli]

Thank you.

Your help was very important. I'll read about MolProbity because after I
calculate of the chi angle, I'll store them in PostgreSQL.

Thanks in advance,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


On Mon, Sep 21, 2009 at 6:18 PM, Steve Darnell <darnells at dnastar.com> wrote:

> Rodrigo,
>
> Perhaps this will get you in the right direction for your
> implementation.  It describes the math for calculating dihedrals and
> defines the chi angle atom mappings for all of the amino acids.  At
> first glance it appears to be correct.  Unfortunately, I don't have any
> code to help you out.
>
> http://www.math.fsu.edu/~quine/IntroMathBio_05/torsion_pdb/torsion_pdb.p
> df<http://www.math.fsu.edu/%7Equine/IntroMathBio_05/torsion_pdb/torsion_pdb.p%0Adf>
>
> If you're only interested in calculating the chi angles only once or
> twice, you could try MolProbity.
>
> http://molprobity.biochem.duke.edu/
>
> Maybe some else knows of another already implemented solution?
>
> ~Steve
>
>
> -----Original Message-----
> From: biopython-bounces at lists.open-bio.org
> [mailto:biopython-bounces at lists.open-bio.org] On Behalf Of Rodrigo
> faccioli
> Sent: Monday, September 21, 2009 2:24 PM
> Cc: biopython
> Subject: Re: [Biopython] Protein side-chain angles from a PDB file
>
> Steve Darnell and Peter Cock,
>
> I apologize your answers. I have complicated my question because I have
> not understood very well about these angles. However, I have understood
> more.
>
> Thus, I'll retype my original question: How can I calculate the
> rotational conformations (rotamers) when I have a PDB file?
>
> Therefore, if I understood better, I need to know which amino acid I'm
> working because the number of chi angles vary according to each amino
> acids.
>
>
> Thanks in advance,
>
> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL Intelligent System in
> Structure Bioinformatics http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
>
>
> On Mon, Sep 21, 2009 at 12:03 PM, Steve Darnell
> <darnells at dnastar.com>wrote:
>
> > Rodrigo,
> >
> > This is just to expand on Peter's comment.  Your original question
> > implicitly mentioned two types of angles: bond and dihedral angles.  A
>
> > bond angle can be calculated with three atoms, two vectors, and a dot
> > product (the first type mentioned).  When you use the term phi and psi
>
> > angles, you are mentioning dihedral (or torsion) angles (the angle
> > betweeen two planes where the intersection is along the bond of
> > interest).  It's more complicated to calculate, but relatively
> straight forward:
> >
> > http://en.wikipedia.org/wiki/Dihedral_angle
> >
> > Were you originally asking about how to calculate the torsion angles
> > in the side chain?  These are known as the chi angles and are used for
>
> > defining rotational conformations (rotomers).  I'll stop here since
> > I'm guessing I misunderstood your original question.
> >
> > Regards,
> > Steve
> >
> > --
> > Steve Darnell
> > DNASTAR, Inc.
> > Madison, WI USA
> >
> >
> > -----Original Message-----
> > From: biopython-bounces at lists.open-bio.org [mailto:
> > biopython-bounces at lists.open-bio.org] On Behalf Of Peter Cock
> > Sent: Monday, September 21, 2009 4:19 AM
> > To: Rodrigo faccioli
> > Cc: biopython
> > Subject: Re: [Biopython] Protein side-chain angles from a PDB file
> >
> > On Sun, Sep 20, 2009 at 8:24 PM, Rodrigo faccioli <
> > rodrigo_faccioli at uol.com.br> wrote:
> > > Hi,
> > >
> > > I have a doubt about how can I calculate the protein side-chain
> > > angles from a PDB file?
> > >
> > > I've read the Bio.PDB.Vector evaluates the angles from three atoms.
> > > However, my question is how can I  chose these atoms from a PDB
> file?
> > >
> > > I have based on peter cook web-site and I have calculated the
> > > phi-psi angles but I haven't seen about side-chain angles.
> >
> > http://www.warwick.ac.uk/go/peter_cock/python/ramachandran/calculate/
> >
> > Its "Cock", not "Cook", but its a common mistake ;)
> >
> > > Sorry if my question is very basic. However, I'm a computer
> > > scientist novice in chemistry issue.
> >
> > How are you defining the side chain angle? From memory (without
> > checking the details), you have the protein back bone which includes
> > the "alpha carbon" (CA in PDB files) to which the side chains are
> > attached. I guess you want to measure the angle of the side chain to
> > the C-alpha to (either of
> > the) neighbouring backbone atoms.
> > The point here is off the top of my head there are at least two
> > possible angles you might be asking about.
> >
> > But in terms of the code, you'll just need to get the coordinates of
> > the three atoms defining the angle (which probably will be the C-alpha
>
> > and two others), which defines two vectors, then take their dot
> > product and thus get the cosine of the angle. Looking at the Psi-Phi
> code should help here.
> >
> > Peter
> >
> > _______________________________________________
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> >
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