Troels,
Commonly I run pymol scripts by means of
run script.py
or
@ script.py
from PyMol shell!
then I use script_command ( e.g findSeq ) and further script syntax for my
tasks
e.g findSeq s.g 1f88
works perfect but
the above command for the ensemmble of pdbs give me error.
James
2012/1/16 Troels Emtekær Linnet <tlin...@gmail.com>
> It depends on, if you run or import the script. The namespace will be
> different.
>
> What do you do?
>
> This is no error. This is basic Python knowledge.
>
> Troels Emtekær Linnet
> Slotsvej 2
> 4300 Holbæk
> Mobil: +45 60210234
>
>
>
> 2012/1/16 James Starlight <jmsstarli...@gmail.com>
>
>> Hi Troels!
>>
>> I've tried to use
>>
>> for x in cmd.get_names(): findSeq.findSeq("QTG", x, "sele_"+x, firstOnly=1)
>>
>>
>>
>> but I obtained error
>>
>> NameError: name 'findSeq' is not defined
>>
>> At the same time just
>>
>> findSeq QTG, 3sn6
>>
>> wokrs perfect
>>
>> 2012/1/14 Troels Emtekær Linnet <tlin...@gmail.com>
>>
>>> Hi James.
>>>
>>> I moved the script under the git repository yesterday, and took care of
>>> the bug.
>>> The script look a little different now.
>>>
>>> So try the new one again from:
>>> http://www.pymolwiki.org/index.php/findseq<http://www.pymolwiki.org/index.php/Findseq>
>>>
>>> The follow the guide on the page.
>>>
>>> # Find the regular expression:# ..H[TA]LVWH# in the few proteins loaded.#
>>> I then showed them as sticks and colored them to highlight matched AAsfor x
>>> in cmd.get_names(): findseq.findseq("..H[TA]LVWH", x, "sele_"+x,
>>> firstOnly=1)
>>>
>>>
>>>
>>> 2012/1/14 James Starlight <jmsstarli...@gmail.com>
>>>
>>>> Jason, hello!
>>>>
>>>> Also I've found possible fix for that bug by lpacing this line in the
>>>> 47 line of the script
>>>>
>>>> if type(selName)!=(types.StringType) and
>>>> type(selName)!=(types.NoneType):
>>>>
>>>>
>>>> By the way I've found another bug when I've tried to find the same
>>>> motifs in the several homolugues structures.
>>>>
>>>> E.g I have 5 structures wich all have motiv S.G where . is the random
>>>> amino acid. When I've tried
>>>>
>>>> findseq S.G, all
>>>>
>>>> the script find that motifs only for last fetched structure. How I could
>>>> solve it?
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Thanks again,
>>>>
>>>> James
>>>>
>>>>
>>>>
>>>> 2012/1/13 Jason Vertrees <jason.vertr...@schrodinger.com>
>>>>
>>>>> James,
>>>>>
>>>>> First, there's a bug in the script. It's not dealing with selName
>>>>> correctly. To get around this just provide something to selName:
>>>>>
>>>>> findSeq S.G, 1a3h, selName=found_seq
>>>>>
>>>>> If findSeq finds the sequence, it'll return the selected atoms in
>>>>> found_seq.
>>>>>
>>>>>
>>>>> Next, SYG is not in that protein. If you search for "S.G" you find
>>>>> SNG. You can double check this by:
>>>>>
>>>>> fStr = cmd.get_fastastr("1a3h")
>>>>>
>>>>> print "SYG" in fStr
>>>>>
>>>>> which return false.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> -- Jason
>>>>>
>>>>>
>>>>> On Fri, Jan 13, 2012 at 1:25 PM, James Starlight <
>>>>> jmsstarli...@gmail.com> wrote:
>>>>> > Dear PyMol Users,
>>>>> >
>>>>> > I need to search defined sequence motifs in my structures.
>>>>> >
>>>>> > For that purpose I've used
>>>>> >
>>>>> > http://www.pymolwiki.org/index.php/FindSeq script
>>>>> >
>>>>> > but when I've try to use it I've got error
>>>>> >
>>>>> > PyMOL>findSeq SYG, 1a3h
>>>>> > Error: selName was not a string.
>>>>> > There was an error with a parameter. Please see
>>>>> > the above error message for how to fix it.
>>>>> >
>>>>> > What I've done wrong? The seqyence Ser Tyr Gly is indeed present in
>>>>> my
>>>>> > structure!
>>>>> >
>>>>> > By the way is there any others way to search for pre-defined
>>>>> sequence motifs
>>>>> > via PyMol?
>>>>> >
>>>>> > Thanks for help,
>>>>> >
>>>>> > James
>>>>> >
>>>>> >
>>>>> ------------------------------------------------------------------------------
>>>>> > RSA(R) Conference 2012
>>>>> > Mar 27 - Feb 2
>>>>> > Save $400 by Jan. 27
>>>>> > Register now!
>>>>> > http://p.sf.net/sfu/rsa-sfdev2dev2
>>>>> > _______________________________________________
>>>>> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>>>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>> > Archives:
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>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Jason Vertrees, PhD
>>>>> PyMOL Product Manager
>>>>> Schrodinger, LLC
>>>>>
>>>>> (e) jason.vertr...@schrodinger.com
>>>>> (o) +1 (603) 374-7120
>>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
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>>>> Save $400 by Jan. 27
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>>>>
>>>
>>>
>>
>
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