On Sat, Sep 17, 2011 at 1:01 AM, Thomas Holder <
[email protected]> 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<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.
>
> Example:
>
> fetch 1d7q, async=0
> as cartoon
> split_states 1d7q
>
Haha... my case got 51 states there. kinda of splendid.
delete 1d7q
> dss all
> rebuild
>
> http://pymolwiki.org/index.**php/Split_States<http://pymolwiki.org/index.php/Split_States>
> http://pymolwiki.org/index.**php/Dss <http://pymolwiki.org/index.php/Dss>
>
> 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
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
>
> Cheers,
> Thomas
>
> lina wrote, On 09/16/11 17:45:
>
> Hi,
>>
>> 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,
>>
>> lina
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
--
Best Regards,
lina
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