pymol-users

[PyMOL] Python scripting for Pymol

[Jerome P. <j.p...@pa...>]

Hi,

I writing a small script in python, in order to export png picture from a MDL
sdfile.
Here is a sample of the function :

def mol2png(ctfile,name):
    pymol.cmd.read_molstr(ctfile,name)
    pymol.cmd.set("valence",1)
    pymol.cmd.color("black","elem c")
    pymol.cmd.color("red","elem o")
    pymol.cmd.color("blue","elem n")
    pymol.cmd.color("yellow","elem s")
    pymol.cmd.bg_color("white")
    pymol.cmd.zoom(name)
    pymol.cmd.png(name)
    time.sleep( 1 )
    pymol.cmd.delete(name)


It works fine only if I have the function time.sleep(1). If not, I have only
empty pictures. Is there another solution to delete the molecule only when
the png file has been written ?

Thanks,

Jerome Pansanel

Re: [PyMOL] Python scripting for Pymol

[gilleain t. <gil...@gm...>]

Hi,

I tried a similar, but simpler, example :

def mol2png(name):
    cmd.png(name)
    cmd.delete(name)

called as 'mol2png("1a2pA")', given that I have an object called "1a2pA"
loaded.

It works just fine on my laptop (mac).

Odd.

gilleain torrance

On 1/6/06, Jerome PANSANEL <j.p...@pa...> wrote:
>
> Hi,
>
> I writing a small script in python, in order to export png picture from a
> MDL
> sdfile.
> Here is a sample of the function :
>
> def mol2png(ctfile,name):
>     pymol.cmd.read_molstr(ctfile,name)
>     pymol.cmd.set("valence",1)
>     pymol.cmd.color("black","elem c")
>     pymol.cmd.color("red","elem o")
>     pymol.cmd.color("blue","elem n")
>     pymol.cmd.color("yellow","elem s")
>     pymol.cmd.bg_color("white")
>     pymol.cmd.zoom(name)
>     pymol.cmd.png(name)
>     time.sleep( 1 )
>     pymol.cmd.delete(name)
>
>
> It works fine only if I have the function time.sleep(1). If not, I have
> only
> empty pictures. Is there another solution to delete the molecule only whe=
n
> the png file has been written ?
>
> Thanks,
>
> Jerome Pansanel
>
>
>
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