VMD-L Mailing List

From: Adam Goler (adamgoler_at_gmail.com)
Date: Fri Mar 21 2014 - 12:21:16 CDT

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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>