I think that the problem is that python is interpreting part of your
directories as special characters. This is due to the fact that Windows
uses the backslash as the directory separator which is also a special
character in python (and in *nix systems).
In a regular python terminal, if I do:
print "C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4))
I get:
C:\\Users\\Brenton\\Documents\\Chem Structures\\PDBs*\x02\x02*HYY -
imatinib\\PyMOL movie\\Image0003.png
Which is not a directory. To fix this, make the string a raw string
(https://docs.python.org/2/reference/lexical_analysis.html#string-literals)
by adding a 'r' before the string like:
print *r*'C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
imatinib\PyMOL movie\Image{}.png'.format(str(i).zfill(4))
Now we get the correct directory:
C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL
movie\Image0003.png
Matt Baumgartner
On 01/06/2015 11:14 AM, Brenton Horne wrote:
I checked, it's not the problem, sadly. Anyway, the first line,
outside the loop, which has the same location saves to Image0001.png
just fine in the correct location without that directory error.
On 7/01/2015 2:11 AM, Matthew Baumgartner wrote:
I think that is because that the directory there doesn't exist. I
think I made a copy paste error of your directory structure.
Please double check, but from your earlier email, it was
C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
imatinib\PyMOL movie\
On 1/6/15, 11:08 AM, Brenton Horne wrote:
I should add that this error occurs for each loop.
On 7/01/2015 2:05 AM, Brenton Horne wrote:
This script gives the error (after the first frame that occurs
before the loop):
ScenePNG-Error: error writing "C:\Users\Brenton\Documents\Chem
Structures\PDBsHYY - imatinib\PyMOL movie\Image0060.png"! Please
check directory...
On 7/01/2015 1:52 AM, Matthew Baumgartner wrote:
Be sure to reply to the list so everyone can benefit from the
questions and answers.
Ah, as Tsjerk mentioned, you need to wrap it in a python-python
end block.
set ray_opaque_background, 0
png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1
python
for i in range(2,61):
cmd.rotate('y', 6)
cmd.png("C:\Users\Brenton\Documents\Chem
Structures\PDBs\2\2HYY - imatinib\PyMOL
movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)
python end
On 01/06/2015 10:40 AM, Brenton Horne wrote:
Sure is this is my code atm:
set ray_opaque_background, 0
png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY -
imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1
for i in range(2,61):
rotate y, 6
cmd.png("C:\Users\Brenton\Documents\Chem
Structures\PDBs\2\2HYY - imatinib\PyMOL
movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)
On 7/01/2015 1:33 AM, Matthew Baumgartner wrote:
Is it in your for loop?
for i in range(2,61):
rotate y, 6
cmd.png("C:\Users\Brenton\Documents\Chem
Structures\PDBs\2\2HYY - imatinib\PyMOL
movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)
On 1/6/15, 10:13 AM, Brenton Horne wrote:
That gave the error:
cmd.png("C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY
- imatinib\PyMOL movie\Image{}.png".format(str(i).zfill(4)),
dpi=300, ray=1)
Traceback (most recent call last):
File "C:\Python27\lib\site-packages\pymol\parser.py", line
464, in parse
exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
File "<string>", line 1, in <module>
NameError: name 'i' is not defined
On 7/01/2015 1:03 AM, Matthew Baumgartner wrote:
cmd.png("C:\Users\Brenton\Documents\Chem
Structures\PDBs\2\2HYY - imatinib\PyMOL
movie\Image{}.png".format(str(i).zfill(4)), dpi=300, ray=1)
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