Re: [PyMOL] succinct secondary structure 'readout'

[gilleain t. <gil...@gm...>]

Hi Tsjerk, Frieda,
I made a different solution (I can't get Tsjerk's to work, oddly - it looks
like it should step through sses correctly, but I can't see why the "
sslist.pop(i)" gives what it should).

Anyway, my 'versions' :) are on the wiki as:

    http://www.pymolwiki.org/index.php/Ss

which is what was asked for. Also, there is a more tricky implementation,
that takes a function and applys it to each sse. I don't know if these
programs are compatible with very early versions of python, bytheway.

    http://www.pymolwiki.org/index.php/Iterate_sses

They were fun to code, anyway.

gilleain torrance

On 10/9/07, Tsjerk Wassenaar <ts...@gm...> 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 < ts...@gm...> 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 < fr...@ns...> 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 <http://www.moleculesinmotion.com>.com<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
>
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