Hi Tsjerk,
I am getting two errors. Is there a problem with line endings? I am
taking the code in emails and on the wiki and pasting it into a text
editor (BBEdit), then copying that and pasting into the PyMOL command
line. The text editor is saving the text with Unix (LF) which I take
to mean Line Feeds.
Here is what PyMOL says -
PyMOL>def ssfilter(sslist):\
PyMOL> i=1\
PyMOL> j=len(sslist)-1\
PyMOL> while i<j:\
PyMOL> if sslist[i][2] == sslist[i+1][2]:\
PyMOL> sslist.pop(i)\
PyMOL> j = j - 1\
PyMOL> else:\
PyMOL> i=i+2\
PyMOL> return sslist
Traceback (most recent call last):
File "/home/local/warren/MacPyMOL070703/build/Deployment/
MacPyMOL.app/pymol/modules/pymol/parser.py", line 257, in parse
File "<string>", line 2
i=1
^
SyntaxError: invalid syntax
PyMOL>sslist=[]
PyMOL>cmd.iterate("n. ca", "sslist.append( [resn,resi,ss] )" )
PyMOL>print ssfilter( sslist )
Traceback (most recent call last):
File "/home/local/warren/MacPyMOL070703/build/Deployment/
MacPyMOL.app/pymol/modules/pymol/parser.py", line 456, in parse
File "<string>", line 1, in ?
NameError: name 'ssfilter' is not defined
Note that when I copy and paste from your email directly, I get a
different error.
Traceback (most recent call last):
File "/home/local/warren/MacPyMOL070703/build/Deployment/
MacPyMOL.app/pymol/modules/pymol/parser.py", line 257, in parse
File "<string>", line 1
def ssfilter(sslist):\
^
SyntaxError: invalid token
That's what prompted me to use the text editor, as it looks like a
line ending problem.
Frieda
On Oct 9, 2007, at 9:07 AM, Tsjerk Wassenaar wrote:
Hi Frieda,
The slash should tell Pymol that the following should be parsed as
python code, but it should work without too, since "while" is a
python keyword. The output you show bothers me. For my case it gives:
[['PRO', '7', 'L'], ['ASP', '8', 'L'], ['PRO', '9', 'H'], ['ALA',
'16', 'H'], ['LEU', '17', 'L'], ['LEU', '26', 'L'],...
which seems to correspond to what you want. In your case the list
"sslist" seems to remain unchanged in the while loop, suggesting
the loop didn't execute.
Maybe a small rewrite:
def ssfilter(sslist):\
i=1\
j=len(sslist)-1\
while i<j:\
if sslist[i][2] == sslist[i+1][2]:\
sslist.pop(i)\
j = j - 1\
else:\
i=i+2\
return sslist
sslist=[]
cmd.iterate("n. ca", "sslist.append( [resn,resi,ss] )" )
print ssfilter( sslist )
Hope it helps (hope it works :S),
Tsjerk
On 10/9/07, Frieda Reichsman <frie...@nsm.umass.edu > wrote:
Hi Tsjerk,
Note the "/" in front of "while", throws an error, I removed it and
got a readout like the following, for each object in the file.
[['MET', '1', 'S'], ['GLN', '2', 'S'], ['VAL', '3', 'S'], ['PHE',
'4', 'S'], ['ILE', '5', 'S'], ['MET', '6', 'S'], ['ARG', '7',
'S'], ...
Thanks,
Frieda
On Oct 9, 2007, at 8:36 AM, Tsjerk Wassenaar wrote:
Hi Frieda,
Okay, caught a flaw in the script. Try:
sslist=[]
cmd.iterate("n. ca", "sslist.append( [resn,resi,ss] )" )
i=1
j=len(sslist)-1
/while i<j:\
if sslist[i][2] == sslist[i+1][2]:\
sslist.pop(i)\
j = j - 1\
else:\
i=i+2
print sslist
#---
Cheers,
Tsjerk
On 10/9/07, Frieda Reichsman <frie...@nsm.umass.edu> wrote:
Hi Tsjerk,
When I paste your script into the command line of PyMol (MacPyMol
to be exact), this is the response:
Traceback (most recent call last):
File "/home/local/warren/MacPyMOL070703/build/Deployment/
MacPyMOL.app/pymol/modules/pymol/parser.py", line 456, in parse
File "<string>", line 2
iterate n. ca, sslist.append( [resn,resi,ss] )
^
SyntaxError: invalid syntax
Is there a way to correct this? (BTW, I am not a python scripter.
I have some experience with javascript, so I see some similarity,
but the syntax is probably going to evade me).
Thanks,
Frieda
On Oct 9, 2007, at 3:35 AM, Tsjerk Wassenaar wrote:
Hi Frieda,
In addition to my previous mail, the following works for me:
sslist=[]
iterate n. ca, sslist.append( [resn,resi,ss] )
/i=1, j=len(sslist)-1
/while i<j:\
if sslist[i][2] == sslist[i+1][2]:\
sslist.pop[i]\
j = j - 1\
else:\
i=i+2
Hope it helps,
Tsjerk
On 10/9/07, Tsjerk Wassenaar < tsje...@gmail.com> wrote:
Hi Frieda,
There's no such command. You'll have to parse the output you get
through a script which filters it in the way you want. This isn't
difficult though (good python exercise :p).
Best,
Tsjerk
On 10/9/07, Frieda Reichsman < frie...@nsm.umass.edu> wrote:
Hi,
I would like to get secondary structure information from a PyMOL
file. I searched the list and found this:
> I need a list of the secondary structure assigned to each
residue by dss in
> pymol. Is there a simple way to write this information to a
file, or dump it
> to the screen?
To dump it to the screen, try:
iterate <object name> & n. ca, print resn,resi,ss
and it works, but the output is a long list of every residue. Is
there a command to get the output more succinctly, such as
1-5 L
6-10 H
11-15 S
Thanks,
Frieda
///////////////////////////////////////////
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
///////////////////////////////////////////
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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
///////////////////////////////////////////
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
///////////////////////////////////////////
--
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
///////////////////////////////////////////
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
///////////////////////////////////////////
--
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
///////////////////////////////////////////
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
///////////////////////////////////////////
