VMD-L Mailing List

From: Adam Goler (adamgoler_at_gmail.com)
Date: Fri Mar 21 2014 - 18:08:49 CDT

I found the dcdplugin.c source code and file reference on (what appears to
be) the VMD plugin API

http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/dcdplugin_8c.html

I will see if I can make any progress using this.

On Fri, Mar 21, 2014 at 11:14 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> It is pretty easy to call the VMD plugins from your own software,
> so rather than hacking the DCD code, I would suggest the use
> of the VMD plugin API, and then you can also write various
> other trajectory formats as well. Various other tool such as
> PyMol, the Gromacs analysis tols, and others make use of
> the VMD plugin API, so there are also many examples of how to do this
> in various ways out in the field.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Mar 21, 2014 at 07:04:58PM +0100, Jérôme Hénin wrote:
> > 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
> > > >>
> > > >>
> > > >> ------------------------------
> > > >> <http://www.avast.com/>
> > > >>
> > > >> Diese E-Mail ist frei von Viren und Malware, denn der avast!
> > > >> Antivirus<http://www.avast.com/>Schutz ist aktiv.
> > > >>
> > > >>
> > > >
> > >
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
> 

-- 
Adam Goler
Graduate Student
Fulmer 126
Dept. of Physics and Astronomy
Washington State University
PO Box 642814
Pullman, WA 99164-2814
Office Phone: (509) 335 7050
adamgoler.com