Hi Gillean, Frieda,

The versions posted on the wiki should work for older versions of Python/Pymol. Don't see why it shouldn't.
Anyway, in my implementation, the pop(i) throws out the element which is the same as the next one, for each element. After that, sslist contains exactly what is requested. Maybe there should've been a 'print sslist' as the final statement.

Cheers,

Tsjerk

On 10/9/07, gilleain torrance <gilleain.torrance@gmail.com> wrote:
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 < tsjerkw@gmail.com> 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 < tsjerkw@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 < friedar@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

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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