On Sat, Sep 17, 2011 at 4:03 AM, Thomas Holder <speleo3@users.sourceforge.net> wrote:
Hi Lina,

>> 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
>     self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>   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

does /home/lina/dssp point to your dssp executable?

Yes.
Later I also tried to keep the dsspcmbi name, still not work.
 

Cheers,
 Thomas

PS: I just realized that there is a new dssp-2 and it does not
understand the -na option, thus will fail with my script without
modifying it.
Thanks for your script.

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



--
Best Regards,

lina