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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Still grepping through log files to find problems?  Stop.
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_______________________________________________
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