Re: [PyMOL] Dynoplot : Interactive plot

2011-08-17 Thread Joseph André 
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 spel...@users.sourceforge.net

 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

 --
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 MPI for Developmental Biology




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[PyMOL] Dynoplot : Interactive plot

2011-08-16 Thread Joseph André 
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.

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Re: [PyMOL] Dynoplot : Interactive plot

2011-08-16 Thread Joseph André 
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 spel...@users.sourceforge.net

 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


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Re: [PyMOL] ball and stick representation of water molecule

2011-07-17 Thread Joseph André 
Dear Leila,

stick_ball setting can only be applied to whole object and not atoms for all
I know.

So, to do ball (oxygen) and sticks (hydrogen) representations is :

show sticks, solvent
show spheres, solvent and e. O
set sphered_scale, 0.3, solvent and e. O

You can adjust the size of the sphere with the last setting.

Hope it will help you.

Joseph



On Sun, Jul 17, 2011 at 1:49 PM, leila karami karami.lei...@gmail.comwrote:

 Dear pymol users


 how to show water molecules as ball and stick representation (O atom: ball
 and H atoms: stick)?


 any help will highly appreciated.


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[PyMOL] Set_toggle ; new script to easily toggle settings

2011-07-14 Thread Joseph André 
Hi PyMOLers,

I was tired of always typing the same commands to change *grid_mode* or *
seq_view*... I know it is possible to use set_key to define action but I
want a key to enable/disable some settings. I wrote a small script that
binds a key to a setting accepting 0/1 or on/off value.

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

It works as is but I'll add other features such as help, check that key is
not already bound, check whether setting is known.

Comments and suggestions are welcome.

Thanks

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Re: [PyMOL] Set_toggle ; new script to easily toggle settings

2011-07-14 Thread Joseph André 
Thank you Thomas

I've updated the scripts following your recommendation.
I wasn't aware of the auto-completion methods. It's great.

Cheers

2011/7/14 Thomas Holder spel...@users.sourceforge.net

 nice :)

 The toggle() function can be much simplified:

 def toggle(setting):
setting_value = cmd.get(setting)
if cmd.toggle_dict.get(setting_**value, 0):
cmd.unset(setting)
else:
cmd.set(setting)

 And you can add auto-completion for the setting name:

 cmd.auto_arg[1].update({
'set_toggle' : cmd.auto_arg[0]['set'],
 })

 Cheers,
  Thomas


 On 07/14/2011 02:10 PM, Joseph André wrote:

 Hi PyMOLers,

 I was tired of always typing the same commands to change *grid_mode* or
 *seq_view*... I know it is possible to use set_key to define action but
 I want a key to enable/disable some settings. I wrote a small script
 that binds a key to a setting accepting 0/1 or on/off value.

 http://pymolwiki.org/index.**php/Set_togglehttp://pymolwiki.org/index.php/Set_toggle

 It works as is but I'll add other features such as help, check that key
 is not already bound, check whether setting is known.

 Comments and suggestions are welcome.

 Thanks

 --
 Joseph ANDRE


 --
 Thomas Holder
 MPI for Developmental Biology




-- 
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33(0)6 75 04 64 00
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