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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> > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > >
> > > >
> > >
> > >
> > > --
> > > 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
