Commonly I run pymol scripts by means of




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.


2012/1/16 Troels Emtekær Linnet <>
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
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2012/1/16 James Starlight <>
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 <>
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:

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 AAs
for x in cmd.get_names(): findseq.findseq("..H[TA]LVWH", x, "sele_"+x, firstOnly=1)

2012/1/14 James Starlight <>
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 <>

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 <> wrote:
> Dear PyMol Users,
> I need to search defined sequence motifs in my structures.
> For that purpose I've used
> 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
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