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
> >
> >
> ------------------------------------------------------------------------------
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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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