VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Mar 21 2014 - 13:04:58 CDT

Hi Adam,

The DCD format is quite straightforward (small global header, then a series of tiny frame headers followed by coordinate arrays, IIRC), so you could reuse some code from the DCD plugin to do the conversion within your program - either interfacing the C++ with python, or possibly just reimplementing a subset of it in pure python.

Cheers,
Jerome

----- Original Message -----
> Hi Ivan,
>
> I am looking into biopython, but I am not sure this is going to help. My
> coordinates are literally a TxNx3 array (T = number of frames in
> trajectory, N = number of alpha carbons, 3 for xyz coordinates). I suppose
> you are right that going from coordinates to PDB as a first step is the way
> to go. Can biopython (or any other tool) do this?
>
> Its looking like I will have to write a script to translate my coordinates
> frame-by-frame into PDB files and then compile them into a DCD (perhaps
> using VMD).
>
> Thanks,
> Adam
> On Mar 21, 2014 5:31 AM, "Ivan Gregoretti" <ivangreg_at_gmail.com> wrote:
>
> > Hi Adam,
> >
> > If I understand your goal correctly, you want to go from an arbitrary
> > object instance to DCD. So, you want
> >
> > adamformat -> DCD
> >
> > I think that you can tackle the problem by doing it in two steps
> >
> > 1) adamformat -> PDB
> >
> > 2) PDB -> DCD
> >
> > For step 1, your best friend is Biopython's Bio.PDB module.
> > http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ
> >
> > For step 2, PDB to DCD, let us hear what the community is currently using.
> > It sounds like a routine task to me.
> >
> > Ivan
> >
> >
> >
> >
> > Ivan Gregoretti, PhD
> > Bioinformatics
> >
> >
> >
> > On Fri, Mar 21, 2014 at 3:51 AM, Norman Geist <
> > norman.geist_at_uni-greifswald.de> wrote:
> >
> >> VMD Main->File->Save Coordinates and choose DCD as file type. Otherwise
> >> have a look at "catdcd".
> >>
> >>
> >>
> >> Norman Geist.
> >>
> >>
> >>
> >> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> >> Auftrag von *Adam Goler
> >> *Gesendet:* Freitag, 21. März 2014 06:00
> >> *An:* Vmd l
> >> *Betreff:* vmd-l: Writing DCD from modified coordinates
> >>
> >>
> >>
> >> Hello,
> >>
> >> I have sets of modified xyz coordinate data (one set for each time step)
> >> from some python output that I would like to convert back into a DCD
> >> trajectory for further analysis in VMD.
> >>
> >> Can anyone offer suggestions on how to go about this?
> >>
> >> Thanks,
> >> Adam
> >>
> >>
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>