pymol-users

[PyMOL] Scripts on Mac

[Sadler, E. <ES...@do...>]

I can run scripts by pasting them, but they fail when I try to read them
from a file, as in:

PyMOL> run ~/scriptfolder/rasmolify.py

This generates lots of errors:

Traceback (most recent call last):
  File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py", line 333,
in parse

parsing.run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names)
  File "/Applications/MacPyMOL.app/pymol/modules/pymol/parsing.py", line
456, in run_file
    execfile(file,global_ns,local_ns)
  File "/Users/evansadler/pymolscripts/rasmolify.py", line 3

     ^
 SyntaxError: invalid syntax

Some result for MacPyMOL and X11 hybrid

What am I doing wrong?

Evan
--
J. Evan Sadler, M.D., Ph.D.
Howard Hughes Medical Institute
Washington University
660 S. Euclid Ave., Box 8022
St. Louis, MO   63110
Tel: 314-362-9067
FAX: 314-454-3012
email: es...@wu...

Re: [PyMOL] Scripts on Mac

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

Hmm. Running scripts has always worked for me on a mac.

Could it be a tab/space problem, or just a character missing at the
end from a copy/paste?

gilleain torrance

On Thu, Feb 28, 2008 at 2:50 PM, Sadler, Evan <ES...@do...> wrote:
> I can run scripts by pasting them, but they fail when I try to read them
>  from a file, as in:
>
>  PyMOL> run ~/scriptfolder/rasmolify.py
>
>  This generates lots of errors:
>
>  Traceback (most recent call last):
>   File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py", line 333,
>  in parse
>
>  parsing.run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names)
>   File "/Applications/MacPyMOL.app/pymol/modules/pymol/parsing.py", line
>  456, in run_file
>     execfile(file,global_ns,local_ns)
>   File "/Users/evansadler/pymolscripts/rasmolify.py", line 3
>
>      ^
>   SyntaxError: invalid syntax
>
>  Some result for MacPyMOL and X11 hybrid
>
>  What am I doing wrong?
>
>  Evan
>  --
>  J. Evan Sadler, M.D., Ph.D.
>  Howard Hughes Medical Institute
>  Washington University
>  660 S. Euclid Ave., Box 8022
>  St. Louis, MO   63110
>  Tel: 314-362-9067
>  FAX: 314-454-3012
>  email: es...@wu...
>
>
>
>  -------------------------------------------------------------------------
>  This SF.net email is sponsored by: Microsoft
>  Defy all challenges. Microsoft(R) Visual Studio 2008.
>  http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>  _______________________________________________
>  PyMOL-users mailing list
>  PyM...@li...
>  https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Re: [PyMOL] Scripts on Mac

[Sadler, E. <ES...@do...>]

That sounds reasonable to me but I know next to nothing about python.
Maybe I should have included the misbehaving script, which was taken directly from the PyMOL wiki script library:

## This is just a quick hack. For something more meaty see;
## http://arcib.dowling.edu/sbevsl/

## Version 0.0.00-000/1


## Turn off the virtual_trackball
cmd.set("virtual_trackball", "off")


## spacefill
def spacefill(p1=''):
    if(p1=='off'):
        cmd.hide("spheres")
    elif(p1==''):
        cmd.show("spheres")
    else:
        print("feh!")
cmd.extend("spacefill", spacefill)

## cartoon
def cartoon(p1=''):
    if(p1=='off'):
        cmd.hide("cartoon")
    elif(p1==''):
        cmd.show("cartoon")
    else:
        print("feh!")
cmd.extend("cartoon", cartoon)

## wireframe
def wireframe(p1=''):
    if(p1=='off'):
        cmd.hide("lines")
    elif(p1==''):
        cmd.show("lines")
    else:
        print("feh!")
cmd.extend("wireframe", wireframe)


## exit
def exit():
    cmd.quit()
cmd.extend("exit", exit)

Any part of it works fine when pasted, but no part works when invoked by "run..."

Evan




On 2/28/08 10:02 PM, "gilleain torrance" <gil...@gm...> wrote:

Hmm. Running scripts has always worked for me on a mac.

Could it be a tab/space problem, or just a character missing at the
end from a copy/paste?

gilleain torrance

On Thu, Feb 28, 2008 at 2:50 PM, Sadler, Evan <ES...@do...> wrote:
> I can run scripts by pasting them, but they fail when I try to read them
>  from a file, as in:
>
>  PyMOL> run ~/scriptfolder/rasmolify.py
>
>  This generates lots of errors:
>
>  Traceback (most recent call last):
>   File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py", line 333,
>  in parse
>
>  parsing.run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names)
>   File "/Applications/MacPyMOL.app/pymol/modules/pymol/parsing.py", line
>  456, in run_file
>     execfile(file,global_ns,local_ns)
>   File "/Users/evansadler/pymolscripts/rasmolify.py", line 3
>
>      ^
>   SyntaxError: invalid syntax
>
>  Some result for MacPyMOL and X11 hybrid
>
>  What am I doing wrong?
>
>  Evan
>  --
>  J. Evan Sadler, M.D., Ph.D.
>  Howard Hughes Medical Institute
>  Washington University
>  660 S. Euclid Ave., Box 8022
>  St. Louis, MO   63110
>  Tel: 314-362-9067
>  FAX: 314-454-3012
>  email: es...@wu...
>
>
>
>  -------------------------------------------------------------------------
>  This SF.net email is sponsored by: Microsoft
>  Defy all challenges. Microsoft(R) Visual Studio 2008.
>  http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>  _______________________________________________
>  PyMOL-users mailing list
>  PyM...@li...
>  https://lists.sourceforge.net/lists/listinfo/pymol-users
>

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Re: [PyMOL] Scripts on Mac

[DeLano S. <de...@de...>]

Evan,
 
Hmm -- the code you posted seems to work just fine with the "run" command
when saved as a text file, so my next guess is that perhap you're saving the
script as something other than text? (RTF perhaps?)
 
HINT: If using TextEdit, select "Make Plain Text" from the Format menu.
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Sadler, Evan
Sent: Friday, February 29, 2008 7:17 AM
To: gilleain torrance; pymol-users
Subject: Re: [PyMOL] Scripts on Mac


That sounds reasonable to me but I know next to nothing about python.
Maybe I should have included the misbehaving script, which was taken
directly from the PyMOL wiki script library:

## This is just a quick hack. For something more meaty see;
## http://arcib.dowling.edu/sbevsl/
 
## Version 0.0.00-000/1
 
 
## Turn off the virtual_trackball
cmd.set("virtual_trackball", "off")
 
 
## spacefill
def spacefill(p1=''):
    if(p1=='off'):
        cmd.hide("spheres")
    elif(p1==''):
        cmd.show("spheres")
    else:
        print("feh!")
cmd.extend("spacefill", spacefill)
 
## cartoon
def cartoon(p1=''):
    if(p1=='off'):
        cmd.hide("cartoon")
    elif(p1==''):
        cmd.show("cartoon")
    else:
        print("feh!")
cmd.extend("cartoon", cartoon)
 
## wireframe
def wireframe(p1=''):
    if(p1=='off'):
        cmd.hide("lines")
    elif(p1==''):
        cmd.show("lines")
    else:
        print("feh!")
cmd.extend("wireframe", wireframe)
 
 
## exit
def exit():
    cmd.quit()
cmd.extend("exit", exit)

Any part of it works fine when pasted, but no part works when invoked by
"run..."

Evan




On 2/28/08 10:02 PM, "gilleain torrance" <gil...@gm...>
wrote:



Hmm. Running scripts has always worked for me on a mac.

Could it be a tab/space problem, or just a character missing at the
end from a copy/paste?

gilleain torrance

On Thu, Feb 28, 2008 at 2:50 PM, Sadler, Evan <ES...@do...> wrote:
> I can run scripts by pasting them, but they fail when I try to read them
>  from a file, as in:
>
>  PyMOL> run ~/scriptfolder/rasmolify.py
>
>  This generates lots of errors:
>
>  Traceback (most recent call last):
>   File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py", line
333,
>  in parse
>
>
parsing.run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names)
>   File "/Applications/MacPyMOL.app/pymol/modules/pymol/parsing.py", line
>  456, in run_file
>     execfile(file,global_ns,local_ns)
>   File "/Users/evansadler/pymolscripts/rasmolify.py", line 3
>
>      ^
>   SyntaxError: invalid syntax
>
>  Some result for MacPyMOL and X11 hybrid
>
>  What am I doing wrong?
>
>  Evan
>  --
>  J. Evan Sadler, M.D., Ph.D.
>  Howard Hughes Medical Institute
>  Washington University
>  660 S. Euclid Ave., Box 8022
>  St. Louis, MO   63110
>  Tel: 314-362-9067
>  FAX: 314-454-3012
>  email: es...@wu...
>
>
>
>  -------------------------------------------------------------------------
>  This SF.net email is sponsored by: Microsoft
>  Defy all challenges. Microsoft(R) Visual Studio 2008.
>  http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>  _______________________________________________
>  PyMOL-users mailing list
>  PyM...@li...
>  https://lists.sourceforge.net/lists/listinfo/pymol-users
>

-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
PyMOL-users mailing list
PyM...@li...
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