On Sat, Sep 17, 2011 at 1:01 AM, Thomas Holder <speleo3@users.sourceforge.net> wrote:
Hi Lina,

Hi Thomas,

Thanks for your answering.

as far as I know the secondary structure atom property is not state specific, so you cannot assign per state. But you can split states to individual objects. The DSSP plugin (I guess you are talking about http://www.pymolwiki.org/index.php/DSSP) however does not deal well with multiple objects (Hongbo, can you fix that?). The build-in command "dss" does, maybe you can use that?

dss did not share the same criteria as the dssp, so sometimes if I choose the dssp criteria, lots of residues need alter.


fetch 1d7q, async=0
as cartoon
split_states 1d7q
Haha... my case got 51 states there. kinda of splendid. 

delete 1d7q
dss all


I can also offer you my own dssp script which works with multiple objects, see attachment. It provides the PyMOL commands "dssp" and "stride". Check "help dssp".

Thanks, I tried,

PyMOL>dssp all, /home/lina/dssp, raw=text_type
Traceback (most recent call last):
  File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py", line 254, in parse
  File "dssp.py", line 70, in dssp
    process = Popen([exe, '-na', tmpfilepdb], stdout=PIPE)
  File "/usr/lib/python2.6/subprocess.py", line 623, in __init__
    errread, errwrite)
  File "/usr/lib/python2.6/subprocess.py", line 1141, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

I am not experienced to fix it, can you provide me some clue.
$ python
python              python2.7-config    python3.2mu
python2.5           python3             python3.2mu-config
python2.5-config    python3.1           python3-config
python2.6           python3.1-config    python-config
python2.6-config    python3.2          
python2.7           python3.2-config



lina wrote, On 09/16/11 17:45:


a quick question,

how can update the ss for all states, not check one by one,

and run dssp and update ...

Thanks for any advice,

Best Regards,


Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Best Regards,