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,


2012/1/13 Jason Vertrees <jason.vertrees@schrodinger.com>

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.


-- 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
> ------------------------------------------------------------------------------
> 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: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120