pymol-users

[PyMOL] Dynoplot : Interactive plot

[Joseph A. <and...@gm...>]

Hi everybody,

I want to build an interactive plot I tried to use and tweak dynoplot but
DynoPlot doesn't work properly : I can display the Tk window but points
aren't plotted. However the dihedrals angles are computed correctly. There
isn't any traceback or error reported on the console.

Do you have experienced similar problems ?

My final goal is to obtain an interactive plot to show b-factor (or value
stored in b-factor column using data2bfactor) in 2D and in 3D.

Thanks.

-- 
Joseph ANDRE

Re: [PyMOL] Dynoplot : Interactive plot

[Thomas H. <sp...@us...>]

On 08/16/2011 03:16 PM, Joseph André wrote:
> Hi everybody,
>
> I want to build an interactive plot I tried to use and tweak dynoplot
> but DynoPlot doesn't work properly : I can display the Tk window but
> points aren't plotted. However the dihedrals angles are computed
> correctly. There isn't any traceback or error reported on the console.
>
> Do you have experienced similar problems ?

I can confirm that DynoPlot does not work. This needs to be fixed.

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology

Re: [PyMOL] Dynoplot : Interactive plot

[Thomas H. <sp...@us...>]

Hi,

I reworked the broken DynoPlot script.

Changes and improvements include:

  * much faster calculation of Phi/Psi angles
  * can open multiple plot windows
  * center on residue with right-mouse-click
  * different plot symbols for GLY and PRO

http://pymolwiki.org/index.php/DynoPlot

Cheers,
   Thomas

Thomas Holder wrote, On 08/16/11 15:51:
> On 08/16/2011 03:16 PM, Joseph André wrote:
>> Hi everybody,
>>
>> I want to build an interactive plot I tried to use and tweak dynoplot
>> but DynoPlot doesn't work properly : I can display the Tk window but
>> points aren't plotted. However the dihedrals angles are computed
>> correctly. There isn't any traceback or error reported on the console.
>>
>> Do you have experienced similar problems ?
> 
> I can confirm that DynoPlot does not work. This needs to be fixed.
> 
> Cheers,
>   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Re: [PyMOL] Dynoplot : Interactive plot

[Joseph A. <and...@gm...>]

Hi Thomas,

thanks for your quick reply. I'm a newbie at Tk programming but from what I
understand, gui code for Dynoplot had been written from scratch. Do you know
if they are libraries that would facilitate the plotting and the interaction
with pymol?

Best regards

Joseph

2011/8/16 Thomas Holder <sp...@us...>

> On 08/16/2011 03:16 PM, Joseph André wrote:
>
>> Hi everybody,
>>
>> I want to build an interactive plot I tried to use and tweak dynoplot
>> but DynoPlot doesn't work properly : I can display the Tk window but
>> points aren't plotted. However the dihedrals angles are computed
>> correctly. There isn't any traceback or error reported on the console.
>>
>> Do you have experienced similar problems ?
>>
>
> I can confirm that DynoPlot does not work. This needs to be fixed.
>
> Cheers,
>  Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
>

-- 
Joseph ANDRE

Re: [PyMOL] Dynoplot : Interactive plot

[Thomas H. <sp...@us...>]

Hi Joseph,

> thanks for your quick reply. I'm a newbie at Tk programming but from
> what I understand, gui code for Dynoplot had been written from scratch.
> Do you know if they are libraries that would facilitate the plotting and
> the interaction with pymol?

There are many libraries for plotting, for example matplotlib which is 
also shipped with recent PyMOL versions.

Dynoplot however also could update the structure by dragging dots on the 
plot, I'm not aware of a plotting library that provides this 
functionality (which does not mean that none such exists :) ).

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology

Re: [PyMOL] Dynoplot : Interactive plot

[Joseph A. <and...@gm...>]

Hi Thomas,

I've read a bit about matplotlib and it seems possible to have interactive
plot. However I don't know if it can interact with pymol.
I'll have a look at it.

Thanks

2011/8/16 Thomas Holder <sp...@us...>

> Hi Joseph,
>
>
>  thanks for your quick reply. I'm a newbie at Tk programming but from
>> what I understand, gui code for Dynoplot had been written from scratch.
>> Do you know if they are libraries that would facilitate the plotting and
>> the interaction with pymol?
>>
>
> There are many libraries for plotting, for example matplotlib which is also
> shipped with recent PyMOL versions.
>
> Dynoplot however also could update the structure by dragging dots on the
> plot, I'm not aware of a plotting library that provides this functionality
> (which does not mean that none such exists :) ).
>
>
> Cheers,
>  Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
>



-- 
Joseph ANDRE
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