Try this.
import subprocess
# propkaprocess
# shell=False controls that the process remains in the same thread.
propkap = Popen(['propka'],
stdin=open('1pdb.pdb', 'r')
stdout=subprocess.PIPE
stderr=subprocess.PIPE
shell=False)
pr
Thanks Jason. But still no luck...
So, I changed it to a python script. It was important that the ending of the
file is .py :-)
But, I can see from the list of objects, that PyMOL fetches the next protein
before it has finished propka first.
Does pymol run external script in some kind of asynchron
Well, I cant get it to work.
Pymol speeds ahead of calling propka.propka
Can you give an example of subprocess?
---
import propka
python
resis = [["1bj6","36"],["1bj6","39"]]
#resis =
[["1bj6","36"],["1bj6","39"],["1bj6","49"],["1ag1","14"],["1gu9","133"],["1gu9","130"],[
you may want to check out the Popen class from the subprocess module...
hth
Martin
On 23.08.11 10:48, Troels Emtekær Linnet wrote:
Hi.
If one writes a pymol script, and calls an external function, the
pymol script continues its operation before waiting for the "success"
of the external functi
Hi Troels,
Try putting your script inside a 'python' block:
python
your commands here...
python end
PyMOL also has a 'sync' command (http://pymolwiki.org/index.php/Sync).
I prefer python blocks.
Cheers,
-- Jason
2011/8/23 Troels Emtekær Linnet :
> Hi.
>
> If one writes a pymol script, and cal
Hi.
If one writes a pymol script, and calls an external function, the pymol
script continues its operation before waiting for the "success" of the
external function.
Is it possible to give a keyword, so it "waits" for the external function
before preceding?
Kind of the same function with:
fetch
Hi,
yes it worked. that mistake is so shameful ... :P
thanks
andrea
2005/6/30, lie...@ultr.vub.ac.be :
> On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote:
> > from pymol import cmd
> > file=open("file.nam")
> > for i in file.readlines():
> > cmd.load(i)
>
> You may have to strip the tr
On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote:
> from pymol import cmd
> file=open("file.nam")
> for i in file.readlines():
> cmd.load(i)
You may have to strip the trailing newline ("\n") from each file name by using
"cmd.load(i.strip())".
Hope this helps,
--
Lieven Buts
Vrije Univ
On Thursday 30 June 2005 13:26, Andrea Spitaleri wrote:
> from pymol import cmd
> file=open("file.nam")
> for i in file.readlines():
> cmd.load(i)
You may have to strip the trailing newline ("\n") from each file name by using
"cmd.load(i.strip())".
Hope this helps,
--
Lieven Buts
Vrije Univ
Hi
this is my "unsuccessful" first script for pymol.
I have a series of files: prot1.pdb prot4.pdb prot55.pdb and so on I'd
like to open them using a loop (instead to open one by one)
I cat them to a file and then I tried to open all of them in pymol:
from pymol import cmd
file=open("file.nam")
fo
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