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.vertrees@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 <jmsstarlight@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.Vertrees@schrodinger.com
(o) +1 (603) 374-7120