Thanks. It works now.
---- Original message ----
>Date: Tue, 7 Jul 2009 18:11:56 +0200
>From: Tsjerk Wassenaar <tsje...@gmail.com>
>Subject: Re: [PyMOL] unexpected EOF while parsing
>To: jo...@uchicago.edu, pymol-users
<pymol-users@lists.sourceforge.net>
>
>Hi Jouko,
>
>You were writing a python script. Now Pymol API can handle basic
>Python, but it's not a one-to-one Python interpreter. To include
>blocks you have to do more than indentation. You have to put
a slash
>in front of the for statement and end all but the of the
blocks with a
>backslash. When trying to do programming, better stick to
Python. Save
>the following as script.py and use run script.py from within
Pymol or
>just issue 'pymol script.py':
>
>from pymol import cmd
>
>z=-7.653
>inc=0.5
>Sections=100
>FirstToLast=range(100)
>for j in FirstToLast:
>
pdb="/home/jouko/DensityCube_Lysozyme2-4a/DensityCube_Lysozyme2-4a_"
>+ str(z) + ".pdb"
> cmd.load(pdb)
> cmd.do("@/home/jouko/b_color8.plm")
> cmd.png(pdb+".png")
> cmd.delete(pdb)
> z=z+inc
> print z
>
>###
>
>Cheers,
>
>Tsjerk
>
>On Tue, Jul 7, 2009 at 5:47 PM, <jo...@uchicago.edu> wrote:
>> Thanks to you and Gregori Gerebtzoff, I can now load the pdb,
>> color the image, and save it as a picture. However I can only
>> do that for the first cross section. I am still getting the
>> unexpected EOF error. I did have the line indented after the
>> loop. I think that maybe when I copied and pasted the script
>> to the email the tab was lost, so this time I am adding the
>> script file as an attachment.
>>
>> Thanks,
>>
>> Jouko
>>
>> P.S. I found that @/home/jouko/b_color8.plm and
>> cmd.do("@/home/jouko/b_color8.plm") both work.
>>
>> ---- Original message ----
>>>Date: Tue, 7 Jul 2009 09:17:53 +0200
>>>From: Tsjerk Wassenaar <tsje...@gmail.com>
>>>Subject: Re: [PyMOL] unexpected EOF while parsing
>>>To: jo...@uchicago.edu
>>>Cc: pymol-users@lists.sourceforge.net
>>>
>>>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...@uchicago.edu> 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
>>>>
>>>>
>>
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>>>>
>>>
>>>
>>>
>>>--
>>>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
>>
>
>
>
>--
>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
------------------------------------------------------------------------------
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
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