Can Jason set up the list as the automatic Reply-To: header? Would
make it a lot easier.
-David
On Mar 9, 2010, at 5:53 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> I never get used to Pymol doing reply-to-sender in stead of reply-to-
> list.... :|
>
> ---------- Forwarded message ----------
> From: Tsjerk Wassenaar <tsje...@gmail.com>
> Date: Tue, Mar 9, 2010 at 11:51 AM
> Subject: Re: [PyMOL] succinct secondary structure 'readout'
> To: Ferdinand Alte <ferdinand.a...@ch.tum.de>
>
>
> Hi Ferdi,
>
> Maybe this works better... Save the code below as ss.py and in pymol
> issue 'run ss.py'. Do make sure to have the path right. In your mail
> you had a path with both \ and /, which might have caused problems.
> After having run the script, you'll have a new command, and you can
> say do 'ss' to get the list for everything or 'ss c. A' to get the
> list only for chain A. Note that there is no check for chain breaks.
> If you do something like 'ss ss h' you'll just get one line, which in
> my case said '56-435 H'. :p Anyone feeling for it, may complicate the
> code by adding checks for chain breaks and such. Yes, this _is_ just a
> hack :)
>
> Hope it helps,
>
> Tsjerk
>
> #-----------ss.py----------
>
> def ss(selection="all"):
> l = [(i.resi,i.ss) for i in cmd.get_model(selection+" and n.
> ca").atom]
> ss = [[l[0][0],l[0][0],l[0][1]]]
> for i in l:
> if i[1] == ss[-1][2]:
> ss[-1][1] = i[0]
> else:
> ss.append([i[0],i[0],i[1]])
> print "\n".join(["%s-%s %s" % (i[0],i[1],i[2] or "L") for i in ss])
>
> cmd.extend("ss", ss)
>
>
> On Tue, Mar 9, 2010 at 8:59 AM, Ferdinand Alte <ferdinand.a...@ch.tum.de
> > wrote:
>> Hi,
>>
>>
>>
>> I would like to get secondary structure information from a PyMol
>> file. I
>> know that the following command gives a long list of every residue:
>>
>>
>>
>>>> iterate <object name> & n. ca, print resn,resi,ss
>>
>>
>>
>>
>>
>> I found the following script, that gives you a more “condensed”
>> list (see
>> below):
>>
>>
>>
>>
>>
>>>> PyMOL>@../..\ss.pml
>>
>>>> PyMOL>class SSList:\
>>
>>>> PyMOL>list = []\
>>
>>>> PyMOL>def purge( self, resi, ss ):\
>>
>>>> PyMOL>if not self.list or self.list[-1][0] != ss:\
>>
>>>> PyMOL>self.list.append( [ss, resi, resi ] )\
>>
>>>> PyMOL>else:\
>>
>>>> PyMOL>self.list[-1][2] = resi\
>>
>>>> PyMOL>def __repr__( self ):\
>>
>>>> PyMOL>return "\n".join( map( self.repr_item, self.list ) )\
>>
>>>> PyMOL>def repr_item( self, item ):\
>>
>>>> PyMOL>return item[0]+" ("+item[1]+"-"+item[2]+")"
>>
>>>> PyMOL>sslist = SSList()
>>
>>>> PyMOL>cmd.iterate( "n. ca", "sslist.purge( resi, ss )" )
>>
>>>> PyMOL>print sslist
>>
>>>> L (2-3)
>>
>>>> H (4-14)
>>
>>>> L (15-23)
>>
>>>> H (24-44)
>>
>>>> L (45-50)
>>
>>>> H (51-72)
>>
>>>> L (73-73)
>>
>>>> H (74-84)
>>
>>>> L (85-86)
>>
>>
>>
>> I have two problems: the command >> PyMOL>@../..\ss.pml << gives the
>> following answer in PyMol: “No such file or directory”
>>
>> When I leave this command away, and I copy & paste the initial
>> iteration
>> followed by the script,
>>
>>
>>
>> iterate SH3 & n. ca, print resn,resi,ss
>>
>> class SSList:\
>>
>> list = []\
>>
>> def purge( self, resi, ss ):\
>>
>> if not self.list or self.list[-1][0] != ss:\
>>
>> self.list.append( [ss, resi, resi ] )\
>>
>> else:\
>>
>> self.list[-1][2] = resi\
>>
>> def __repr__( self ):\
>>
>> return "\n".join( map( self.repr_item, self.list ) )\
>>
>> def repr_item( self, item ):\
>>
>> return item[0]+" ("+item[1]+"-"+item[2]+")"
>>
>> sslist = SSList()
>>
>> cmd.iterate( "n. ca", "sslist.purge( resi, ss )" )
>>
>> print sslist
>>
>>
>>
>>
>>
>> PyMol gives me the following answer:
>>
>>
>>
>> Iterate: iterated over 68 atoms.
>>
>> <pymol.SSList instance at 0x000000000688C648>
>>
>>
>>
>>
>>
>> I still get the long list with every single residue mentioned, but
>> not the
>> desired “condensed” form.
>>
>> Maybe I just don’t know how to print the list on the screen. Or is
>> there
>> more about it?
>>
>>
>>
>>
>>
>> Thanks for any help,
>>
>>
>>
>> Ferdi
>>
>>
>>
>> ---
>> ---
>> ---
>> ---------------------------------------------------------------------
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
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>> _______________________________________________
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>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>
> ---
> ---
> ---
> ---------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-
> us...@lists.sourceforge.net
------------------------------------------------------------------------------
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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