Hi Bradley,
> Does "cmd.iterate('all and n. ca', 'stored.stored_ss.append([ss])')"
'ss' in this usage just reads from the current model of the molecule
in memory. PyMOL can read secondary structure from the PDB files if
it's present or determine it by itself using dss. PyMOL defaults to
the former, but can do the latter if you explicitly call 'dss' on your
structure. To illustrate this, in the following snippet you'll get
two different lists of secondary structure:
# grab a protein
fetch 1wld
from pymol import stored
stored.a = []
stored.b = []
iterate *, stored.a.append(ss)
dss
iterate *, stored.b.append(ss)
You will see that the list in stored.a does not equal the list in
stored.b. The first is read from the file, the 2nd from the results
of dss.
Cheers,
-- Jason
On Fri, Jul 23, 2010 at 11:35 AM, Bradley Hintze
<bradle...@aggiemail.usu.edu> wrote:
> I'm writing a manuscript and just need clarification.
>
> Does "cmd.iterate('all and n. ca', 'stored.stored_ss.append([ss])')"
> use pymol's DSS to assign secondary structure? If not, how is this
> command assigning secondary structure?
>
> Thanks,
> Bradley
>
>
> On Tue, Jun 22, 2010 at 7:37 PM, Jason Vertrees
> <jason.vertr...@schrodinger.com> wrote:
>> Hi Bradley,
>>
>> PyMOL uses its own internal routine for secondary structure
>> classification. The iterator token is "ss". Check out
>> http://pymolwiki.org/index.php/Ss and
>> http://pymolwiki.org/index.php/Iterate_sses and
>> http://pymolwiki.org/index.php/WriteSS.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Tue, Jun 22, 2010 at 4:04 PM, Bradley Hintze
>> <bradle...@aggiemail.usu.edu> wrote:
>>> Hi all,
>>>
>>> Is there a way to get an output from PyMol's DSS command (like a dssp
>>> output)?
>>>
>>> --
>>> Bradley J. Hintze
>>> Graduate Student
>>> Duke University
>>> School of Medicine
>>> 801-712-8799
>>>
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>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>
>
>
> --
> Bradley J. Hintze
> Graduate Student
> Duke University
> School of Medicine
> 801-712-8799
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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