> 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.
Actually, nowadays you can just wrap Python blocks with the statements:
"python" and "python end". For example:
# example pymol script an embedded Python block
dele all
reset
python
for i in range(1,10):
print i
cmd.pseudoatom(pos=[i,i,i],color='auto')
python end
zoom (all), 10
show spheres
rock
# use box wizard to create some walls:
refresh
wizard box
cmd.get_wizard().set_mode("walls")
wizard
dele box_points
turn x,-70
turn y,-30
turn z,-10
ray
# end example
Cheers,
Warren
> -----Original Message-----
> From: Tsjerk Wassenaar [mailto:[email protected]]
> Sent: Tuesday, July 07, 2009 9:16 AM
> To: [email protected]; pymol-users
> Subject: Re: [PyMOL] unexpected EOF while parsing
>
> 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, <[email protected]> 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 <[email protected]>
> >>Subject: Re: [PyMOL] unexpected EOF while parsing
> >>To: [email protected]
> >>Cc: [email protected]
> >>
> >>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, <[email protected]> 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 ([email protected])
> >>> Info Page:
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>> Archives:
> > http://www.mail-archive.com/[email protected]
> >>>
> >>
> >>
> >>
> >>--
> >>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
> _______________________________________________
> PyMOL-users mailing list ([email protected])
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/[email protected]
>
>
>
------------------------------------------------------------------------------
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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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