Re: [PyMOL] unexpected EOF while parsing

[Tsjerk W. <ts...@gm...>]

Hi Jouko,

I think you went through the Python and Pymol tutorials a bit too fast
;) You're writing a Python script to be loaded with 'run'. That means
you have to adhere to Python API and can't use the Pymol specific
language. E.g. you can't use 'png pdb', but have to use 'cmd.png(pdb)'
in which case pdb will be treated as a variable rather than a string.
And you definitely can't use '@something.pml'.

The EOF is because you violated one of the basic rules of Python: it
uses indentation to structure programming. Thus after a for loop you
have to start an indented line.

Furthermore:
- range by default starts from 0: range(0,Sections) is equal to range(Sections)
- load will strip .pdb from the filename, so you wouldn't be able to
use the variable pdb to point to it; better specify a name
- png probably adds .png to the name, but it's good to make sure it does

###

from pymol.cgo import *
import colorsys,sys,re
from pymol import cmd

z=-8.153
inc=0.5
Sections=100
for j in range(0, Sections):
    pdb="c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2-4a/DensityCube_Lysozyme2-4a_"+
str(z) + ".pdb"
    load(pdb,pdb)
    cmd.do("@c:/b_color8.plm")
    cmd.png(pdb+".png")
    cmd.delete(pdb)
    z=z+inc

Hope it helps,

Tsjerk

On Tue, Jul 7, 2009 at 3:17 AM, <jo...@uc...> wrote:
> I am new to pymol and python.  I have a number of cross
> sections of lysozyme.  I want to display them one by one,
> color them using a script file that I have written earlier,
> and save the image.  I have written a script file that I had
> hoped would do this.  I have a couple problems with script
> file, but the one that is frustrating me the most is that
> immediately after the beginning of for loop pymol says that
> there in an unexpected EOF.  The other problem is that when I
> try to use the variable pdb, pymol does not use the value of
> the variable, but the variable name itself.  I have pasted my
> script file below and part of the log file.
>
> from pymol.cgo import *
> import colorsys,sys,re
> from pymol import cmd
>
> z=-8.153
> inc=0.5
> Sections=100
> for j in range(0, Sections):
>
> pdb="c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2-4a/DensityCube_Lysozyme2-4a_"
> + str(z) + ".pdb"
>      load pdb
>      @c:/b_color8.plm
>      png pdb
>      delete pdb
>      z=z+inc
>
>
> PyMOL>@c:/Users/jouko/CrossSections.plm
> PyMOL>from pymol.cgo import *
> PyMOL>import colorsys,sys,re
> PyMOL>from pymol import cmd
> PyMOL>z=-8.153
> PyMOL>inc=0.5
> PyMOL>Sections=100
> PyMOL>for j in range(o, Sections):
> Traceback (most recent call last):
>  File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pymol\parser.py", line 256, in parse
>   exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>  File "<string>", line 1
>    for j in range(o, Sections):
>                                ^
> SyntaxError: unexpected EOF while parsing
> PyMOL>pdb="c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2-4a/DensityCube_Lysozyme2-4a_"
> + str(z) + ".pdb"
> PyMOL>load pdb
> ExecutiveProcessPDBFile-Error: Unable to open file 'pdb'.
>
> Thanks in advance for your advice.
>
>
> Jouko
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
> This is your chance to win up to $100,000 in prizes! For a limited time,
> vendors submitting new applications to BlackBerry App World(TM) will have
> the opportunity to enter the BlackBerry Developer Challenge. See full prize
> details at: http://p.sf.net/sfu/blackberry
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623