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
CrossSections.plm
Description: Binary data
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