Hey jin
lian
I guess you need to remove the parentheses before
"self.residue_range". They are not necessary or else, you need to compete those
parentheses. This is not the problem of modeller, rather its mainly related to
python script.
hope this
helps.
Cheers
PanDa
===================================================================
If
your ship doesn't come in, swim out to it.......Jonathan
Winters
===================================================================
Pankaj
R.
Daga
|
Department of Medicinal Chemistry | e-mail:
pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy |
fax:
+1-662-915-5638
University of
Mississippi |
phone: +1-662-915-1853
University,
MS, 38677-1848 |
===================================================================
-----
Original Message -----
From:
<modeller_usage-request@salilab.org>
To:
<modeller_usage@salilab.org>
Sent: Tuesday, April 17, 2007 5:32
AM
Subject: modeller_usage Digest, Vol 6, Issue 33
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> Today's
Topics:
>
> 1. Re: Psi and Phi Dihedral Restraints
(Modeller Caretaker)
> 2. using model-loop-refine in
Modeller9v1 (jinlian05@lzu.cn)
> 3. Re: using
model-loop-refine in Modeller9v1 (Charlie Allerston)
>
>
>
----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 16 Apr 2007 23:40:48 -0700
> From:
Modeller Caretaker <modeller-care@salilab.org>
> Subject: Re:
[modeller_usage] Psi and Phi Dihedral Restraints
> To: Brandon Mills
<bmm25@pitt.edu>
> Cc: modeller_usage@salilab.org
>
Message-ID: <46246BF0.1030209@salilab.org>
> Content-Type:
text/plain; charset=ISO-8859-1; format=flowed
>
> Brandon Mills
wrote:
>> I have recently been toying with certain restraints in my
.rsr files,
>> and I have a couple questions. Can someone elaborate on
the effect of
>> restraints which contain eight atoms and a multiple
of six parameters
>> (I've seen 6, 12, 18, 24, and 30), and the
restraints which contain 4
>> atoms and 28 parameters? What exactly
are these parameters? Also, is
>> there an easy way to pick out the
psi and phi restraints out of the
>> general dihedral restraints?
Thanks in advance!
>
> See
http://salilab.org/modeller/9v1/manual/node382.html for a
> description
of the restraints file format. The second column (restraint
> form) is
the one you're probably interested in (it will be 9 for
> multi-binormal
(phi/psi) restraints). There is a multiple of six
> parameters for each
of these because there are six parameters for each
> well in the function
(weight, 2 means, 2 stdevs, and a correlation; see
>
http://salilab.org/modeller/9v1/manual/node91.html).
>
> The other
restraints you mention are almost certainly cubic spline
> restraints
(form 10). These are used because it is more efficient to
> evaluate a
cubic spline than a multiple Gaussian.
>
> Ben Webb, Modeller
Caretaker
> --
>
modeller-care@salilab.org
http://www.salilab.org/modeller/
> Modeller mail list:
http://salilab.org/mailman/listinfo/modeller_usage
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>
>
------------------------------
>
> Message: 2
> Date: Tue, 17
Apr 2007 16:49:01 +0800
> From: "" <jinlian05@lzu.cn>
>
Subject: [modeller_usage] using model-loop-refine in Modeller9v1
>
To: modeller_usage@salilab.org
> Message-ID:
<376799741.12858@st.lzu.edu.cn>
> Content-Type: text/plain
>
> Hi,
> I am new to modeller and I have trouble creating a homology
model of a
> protein using model-loop-refine. I modified the
model-loop-refine.py script as
> shown below and I got error messages. I
would appreciate it if any one
> can give me any suggestion.
>
Thanks.
>
> from modeller import *
> from modeller.automodel
import *
>
> log.verbose()
> env = environ()
>
>
env.io.atom_files_directory = './:../atom_files'
>
> # Create a new
class based on 'loopmodel' so that we can redefine
> #
select_loop_atoms
> class myloop(loopmodel):
> #
This routine picks the residues to be refined by loop
modeling
> def
select_loop_atoms(self):
>
return selection(self.residue_range('53:',
'67:')
>
(self.residue_range('89:',
'96:')
>
(self.residue_range('118:',
'144:')
>
(self.residue_range('166:',
'177:')
>
(self.residue_range('199:',
'221:')
>
(self.residue_range('243:', '254:'))
>
> a =
myloop(env,
>
alnfile = 'seg.ali', # alignment
filename
>
knowns =
'1u19A',
# codes of the
templates
>
sequence =
'mrg1',
# code of the
target
>
loop_assess_methods=assess.DOPE) # assess each loop with DOPE
>
a.starting_model=
1
# index of the first model
> a.ending_model =
1
# index of the last model
>
> a.loop.starting_model =
1 # First loop
model
> a.loop.ending_model =
2 # Last loop
model
>
>
a.make()
# do modeling and loop refinement
>
> This is the
error:
> File "model-loop-refine.py", line
21
> m = myloop(env,
> ^
>
SyntaxError: invalid syntax
>
>
>
>
>
>
------------------------------
>
> Message: 3
> Date: Tue, 17
Apr 2007 10:32:29 +0000
> From: "Charlie Allerston"
<charlieboyblue@hotmail.com>
> Subject: Re: [modeller_usage] using
model-loop-refine in Modeller9v1
> To: jinlian05@lzu.cn,
modeller_usage@salilab.org
> Message-ID:
<BAY117-F1818D25C2653CF5F52AE3CDD510@phx.gbl>
> Content-Type:
text/plain; charset="us-ascii"
>
> An HTML attachment was
scrubbed...
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>
>
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End of modeller_usage Digest, Vol 6, Issue 33
>
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>
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