Re: [PyMOL] unexpected EOF while parsing
> 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:tsje...@gmail.com]
> Sent: Tuesday, July 07, 2009 9:16 AM
> To: jo...@uchicago.edu; 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, 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
> >>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
> >>
>
Re: [PyMOL] unexpected EOF while parsing
Thanks. It works now.
Original message
>Date: Tue, 7 Jul 2009 18:11:56 +0200
>From: Tsjerk Wassenaar
>Subject: Re: [PyMOL] unexpected EOF while parsing
>To: jo...@uchicago.edu, pymol-users
>
>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, 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
>>>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, 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 ha
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, 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
>>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, 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>@
Re: [PyMOL] unexpected EOF while parsing
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
>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, 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 "", 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 e
Re: [PyMOL] unexpected EOF while parsing
Jouko, Try to use the cmd.load(pdb) command instead of load pdb Apparently, the load statement takes a file name as argument, not a variable, whereas the api call (cmd.load) can handle variables. Best, Grégori -Original Message- From: jo...@uchicago.edu [mailto:jo...@uchicago.edu] Sent: Tuesday, July 07, 2009 3:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] unexpected EOF while parsing 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 "", 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] unexpected EOF while parsing
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, 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 "", 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
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[PyMOL] unexpected EOF while parsing
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 "", 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
