Re: [PyMOL] Problems with FindSeq.py script

[James Starlight]

Troels, thanks again for so detailed explanation

Firstly I've tried to use IMPORT SCRIPT and all of the above commands works
now :)


Now I'd like to understand the main sytnax of the findseq script in more
detailes.

E.g I have the set of homologues protein from wich I'd like to find triplet
motifs wich consist of

Ser or Thr in the first place
Tyr or His or Trp in the second
Gly in the third place

For that purpose I've used the below command

for x in cmd.get_names(): findseq.findseq("[ST][YHW]G", x, "supertest_"+x,
firstOnly=0)

As the result only ONE motiv ( commonly Thr-Tyr-Gly ) was found in each of
my proteins bu as I know that set contains more than this combination of
the choosen amino acids ( e.g motifs Ser-Tyr-Gly or Thr-Trp-Gly ) also
present in my dataset.

Where I've done mistake?
Finally what is the 'firstOnly=0' and where I can obtain information about
syntax of regular expressins used in PyMol?

Thanks again

James

2012/1/16 Troels Emtekær Linnet 

> Dear James.
>
> That is because there are different ways, how to get functions available
> in Python.
> Either you can import a script.py or you can execute it.
>
> If you execute the script.
> In Python, you would do: *execfile("script.py")*
> In PyMOL, a shortcut to this is: *run script.py OR execfile("script.py")*
>
> Then the functions in the script file will be directly available with the
> function names.
> functionname(inp1=A, inp2=B)
>
> If you import the script in Python/Pymol, it will be handled as a module.
> *import script*
> That means, that you have access to functions like this
> script.functionname(inp1=A, inp2=B)
>
> For small scripts, the name of the functions in the file is probably
> similar to the filename of the script.
> Thats why, you would see:
> findseq.findseq(inp1=A, inp2=B)
>
> Then comes the export feature in PyMOL. The line:
> cmd.extend("findseq", findseq )
>
> That means, that PyMOL extends the function name "findseq" to be directly
> accessible in pymol.
> So the functions can be access directly. But you have still both options.
>
> import findseq
> findseq.findseq(inp1=A, inp2=B)
> findseq inp1=A, inp2=B
>
> Notice, that the extend make it possible to call the function directly,
> and making input with spaces.
> This is a little more "human" readable.
>
> But a problem occurs, if you want to parse a variable to the extended
> method.
> Say you write.
>
> import propka
> fetch 4ins, async=0
> proteinname="4ins"   (Your variable)
> propka proteinname  (will not work)
> propka 4ins(will work)
> propka.propka(proteinname)  (will work)
>
> I hope this clarify a little.
>
> Read more about namespaces here:
> http://www.pymolwiki.org/index.php/Running_Scripts
> http://docs.python.org/tutorial/modules.html
>
> Best
> Troels
>
>
> 2012/1/16 James Starlight 
>
>> Troels,
>>
>>
>> Commonly I run pymol scripts by means of
>>
>> run script.py
>>
>> or
>>
>> @ script.py
>>
>> 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.
>>
>> James
>>
>>
>> 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
>>> Slotsvej 2
>>> 4300 Holbæk
>>> Mobil: +45 60210234
>>>
>>>
>>>
>>> 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:
> 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 
>
>> 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 ac

Re: [PyMOL] Problems with FindSeq.py script

[Troels Emtekær Linnet]

Dear James.

That is because there are different ways, how to get functions available in
Python.
Either you can import a script.py or you can execute it.

If you execute the script.
In Python, you would do: *execfile("script.py")*
In PyMOL, a shortcut to this is: *run script.py OR execfile("script.py")*

Then the functions in the script file will be directly available with the
function names.
functionname(inp1=A, inp2=B)

If you import the script in Python/Pymol, it will be handled as a module.
*import script*
That means, that you have access to functions like this
script.functionname(inp1=A, inp2=B)

For small scripts, the name of the functions in the file is probably
similar to the filename of the script.
Thats why, you would see:
findseq.findseq(inp1=A, inp2=B)

Then comes the export feature in PyMOL. The line:
cmd.extend("findseq", findseq )

That means, that PyMOL extends the function name "findseq" to be directly
accessible in pymol.
So the functions can be access directly. But you have still both options.

import findseq
findseq.findseq(inp1=A, inp2=B)
findseq inp1=A, inp2=B

Notice, that the extend make it possible to call the function directly, and
making input with spaces.
This is a little more "human" readable.

But a problem occurs, if you want to parse a variable to the extended
method.
Say you write.

import propka
fetch 4ins, async=0
proteinname="4ins"   (Your variable)
propka proteinname  (will not work)
propka 4ins(will work)
propka.propka(proteinname)  (will work)

I hope this clarify a little.

Read more about namespaces here:
http://www.pymolwiki.org/index.php/Running_Scripts
http://docs.python.org/tutorial/modules.html

Best
Troels


2012/1/16 James Starlight 

> Troels,
>
>
> Commonly I run pymol scripts by means of
>
> run script.py
>
> or
>
> @ script.py
>
> 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.
>
> James
>
>
> 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
>> Slotsvej 2
>> 4300 Holbæk
>> Mobil: +45 60210234
>>
>>
>>
>> 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:
 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 

> 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 
>
>> 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.pymolwik

Re: [PyMOL] Problems with FindSeq.py script

[James Starlight]

Troels,


Commonly I run pymol scripts by means of

run script.py

or

@ script.py

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.

James

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
> Slotsvej 2
> 4300 Holbæk
> Mobil: +45 60210234
>
>
>
> 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:
>>> 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 
>>>
 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 

> 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!
> > 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.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
 ___
 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

>>>
>>>
>>
>
--
RSA(R) Conferen

Re: [PyMOL] Problems with FindSeq.py script

[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:
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 

> 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 
>
>> 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 
>> 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.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
> ___
> 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
>
--
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

Re: [PyMOL] Problems with FindSeq.py script

[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,

James



2012/1/13 Jason Vertrees 

> 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 
> 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.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___
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

Re: [PyMOL] Problems with FindSeq.py script

[Jason Vertrees]

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  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.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
RSA(R) Conference 2012
Mar 27 - Feb 2
Save $400 by Jan. 27
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[PyMOL] Problems with FindSeq.py script

[James Starlight]

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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