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!
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>> > _______________________________________________
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>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>
>
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Mar 27 - Feb 2
> Save $400 by Jan. 27
> Register now!
> http://p.sf.net/sfu/rsa-sfdev2dev2
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