Re: [PyMOL] disconnected loop in pymol

2010-03-04 Thread Eric Larson 
Hi Tassos,

Perhaps your pdb file has something in the segid column?  For some reason Pymol 
cannot draw a connected cartoon if you values in the segid column so simply 
remove them.

hope that solves your problem,

Eric 
__
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MSGPP Consortium
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195

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>   1. disconnected loop in pymol (Anastassis Perrakis)
>
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> Message: 1
> Date: Wed, 3 Mar 2010 15:40:40 +0100
> From: Anastassis Perrakis 
> Subject: [PyMOL] disconnected loop in pymol
> To: 
> Message-ID: <690b3058-e90b-4a06-843c-1dfd50904...@nki.nl>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all,
>
> I have a small domain which is mostly loops, its a Cys-knot.
> All residues are in the preferred Rama regions, and all atoms are
> present in the PDB,
> but Pymol decides to 'break' my cartoon!
>
> Would anyone have a solution to force pymol draw a nice loop where the
> break is?
> (see small image attached)
>
> Thanks in advance,
>
> Tassos
>
>
>
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Re: [PyMOL] disconnected loop in pymol

2010-03-04 Thread vincent Chaptal 
Hi,

I've seen this when using modeller and then working in coot to change
parts of my model. The pdb looked like this:
ATOM  2  CA  ALA A  61  19.187 -16.491  60.818  1.00  7.01
AC
ATOM  3  CB  ALA A  61  17.667 -16.537  61.040  1.00  7.01
AC
ATOM  4  C   ALA A  61  19.475 -16.919  59.419  1.00  7.01
AC
ATOM  5  O   ALA A  61  20.559 -16.678  58.892  1.00  7.01
AO
ATOM  6  N   GLY A  62  18.489 -17.575  58.780  1.00
9.64  N
ATOM  7  CA  GLY A  62  18.677 -18.017  57.433  1.00
9.64  C
ATOM  8  C   GLY A  62  19.240 -19.399  57.475  1.00
9.64  C
ATOM  9  O   GLY A  62  19.501 -20.003  56.436  1.00
9.64  O

The missing 'A' for the GLY at the end of the line was preventing the
cartoon. Writing back the A did the trick.
vincent



Anastassis Perrakis wrote:
> Dear all,
>
> I have a small domain which is mostly loops, its a Cys-knot.
> All residues are in the preferred Rama regions, and all atoms are
> present in the PDB,
> but Pymol decides to 'break' my cartoon!
>
> Would anyone have a solution to force pymol draw a nice loop where the
> break is?
> (see small image attached)
>
> Thanks in advance,
>
> Tassos
>
>
>
>
>
> 
>

--

Vincent Chaptal

Dept. of Physiology at UCLA

http://www.physiology.ucla.edu/Labs/Abramson/index.html


Phone: 1-310-206-1399


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[PyMOL] disconnected loop in pymol

2010-03-04 Thread Anastassis Perrakis 

Dear all,

I have a small domain which is mostly loops, its a Cys-knot.
All residues are in the preferred Rama regions, and all atoms are  
present in the PDB,

but Pymol decides to 'break' my cartoon!

Would anyone have a solution to force pymol draw a nice loop where the  
break is?

(see small image attached)

Thanks in advance,

Tassos



<>

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[PyMOL] Some plugin development questions

2010-03-04 Thread Michael Lerner 
Hi all,

I'm trying to pretty up the next version of the APBS plugin and I've
run into two issues that I'm hoping others have solved:

1. Does anyone have any experience with PMW's OptionMenu? I've been
trying something where I call an OptionMenu's setitem() and it keeps
failing no matter what I do. Perhaps someone can just point me at some
working sample code.

2. I'm having trouble launching command-line Python scripts from my
plugin on OS X. Scripts complain about things like "import time"
failing that work from the command line. I have a wrapper function
that works on Windows, OS X and Linux for normal binaries, and I've
included it below. It looks to me like programs launched via PyMOL
(either via os.system or via subprocess.call) just don't get a proper
environment set up, thus causing Python imports to fail, but I'm not
entirely sure.

I typically work around this in an ugly way: I mess around with
sys.path, import whatever.py and then call whatever.main() directly.
This is obviously quite fragile and depends on whatever.py to have a
nice whatever.main() defined. It gets substantially worse when
whatever.py wants lots of things in its own path.

Has anyone else experienced this? Do you know a nice workaround?

Thanks,

-Michael

def run(prog,args):
'''
wrapper to handle spaces on windows.
prog is the full path to the program.
args is a string that we will split up for you.
or a tuple.  or a list. your call.

return value is (retval,prog_out)

e.g.

(retval,prog_out) = run("/bin/ls","-al /tmp/myusername")
'''
import subprocess,tempfile

if type(args) == type(''):
args = tuple(args.split())
elif type(args) in (type([]),type(())):
args = tuple(args)
args = (prog,) + args

try:
output_file = tempfile.TemporaryFile(mode="w+")  # <--
shouldn't this point to the temp dir
except IOError:
print "Error opening output_file when trying to run the APBS command."

print "Running:\n\tprog=%s\n\targs=%s" % (prog,args)
retcode = 
subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
output_file.seek(0)
#prog_out = output_file.read()
prog_out = ''.join(output_file.readlines())
output_file.close() #windows doesn't do this automatically
if DEBUG:
print "Results were:"
print "Return value:",retcode
print "Output:"
print prog_out
return (retcode,prog_out)

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Bethesda MD 20892-9314 (USPS)

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