VMD-L Mailing List

From: Bachir Aoun (bachir.aoun_at_e-aoun.com)
Date: Fri Jul 25 2014 - 10:34:43 CDT

Dear Josh,
thank you for answering and clarifying my concerns.
you are right. my python version is 2.7 and the one vmd is looking for by
default is a 2.5.

thanks

On Thu, Jul 24, 2014 at 5:54 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Unfortunately its as simple as recompiling VMD with python support, since
> the default binaries distributed don't include it (which is why you can't
> get it to work in all likelihood). Not many people use the python interface
> to VMD (<1% of the VMD install base) since it means you need to compile VMD
> yourself to accommodate your system version of python. If you've ever
> compiled VMD before, its trivial to add it, and the docs are all there
> online on how to use it. If not, I'd encourage you to learn, as it took me
> a weekend to get it all figured out the first time I compiled VMD from
> source. Since then, its probably increased my productivity by an order of
> magnitude, since I can do math on results without going through expr.
> -Josh
> On 7/24/14, 6:13 PM, Bachir Aoun wrote:
>
> I didn't say there isn't, I am aware of vmdnumpy but im not able to make
> it work.
> if you have any example that you can share that would be very helpful.
> any example that would lets say export a numpy array of a selection of
> atoms over a number of configurations (frames)
> something like that: export(atomsIndexes, framesIndexes, outputFileName)
>
> thanks
>
>
> On Thu, Jul 24, 2014 at 5:04 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
>> On Thu, Jul 24, 2014 at 5:33 PM, Bachir Aoun <bachir.aoun_at_e-aoun.com>
>> wrote:
>> > thank you guys,
>> > I already know about MDanalysis, it's a package itself and uses c
>> libraries
>> > to parse dcd files. Since vmd support python I was hoping there is a
>> simple
>> > solution within vmd itself.
>>
>> what makes you think there isn't?
>>
>> >
>> > thanks
>> >
>> >
>> > On Thu, Jul 24, 2014 at 2:59 PM, Ajasja Ljubetič <
>> ajasja.ljubetic_at_gmail.com>
>> > wrote:
>> >>
>> >> Just save the frames into a DCD and load that directly into python
>> using
>> >> https://code.google.com/p/mdanalysis/.
>> >>
>> >>
>> >> On 24 July 2014 20:58, Bachir Aoun <bachir.aoun_at_e-aoun.com> wrote:
>> >>>
>> >>> Hi
>> >>>
>> >>> I am having hard time extracting atoms coordinates from vmd to do some
>> >>> data analysis using python scripts.
>> >>> the way i am doing it right now is to export all trajectory frames in
>> pdb
>> >>> files, read all the pdbf iles with a python script and parse the
>> coordinates
>> >>> into a numpy array.
>> >>>
>> >>> is there any way to directly export an array of atoms coordinates
>> along
>> >>> all trajectory configurations from vmd to a python environment
>> (usually
>> >>> numpy).
>> >>>
>> >>> thanks
>> >>
>> >>
>> >
>> >
>> >
>> > --
>> > Bachir AOUN
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>
>
>
> --
> Bachir AOUN
>
>
> 

-- 
Bachir AOUN