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Re: [modeller_usage] using model-loop-refine in Modeller9v1

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         | 
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----- Original Message -----
From: <>
To: <>
Sent: Tuesday, April 17, 2007 5:32 AM
Subject: modeller_usage Digest, Vol 6, Issue 33


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> Today's Topics:
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>   1. Re: Psi and Phi Dihedral Restraints (Modeller Caretaker)
>   2.  using model-loop-refine in Modeller9v1 ()
>   3. Re: using model-loop-refine in Modeller9v1 (Charlie Allerston)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 16 Apr 2007 23:40:48 -0700
> From: Modeller Caretaker <>
> Subject: Re: [modeller_usage] Psi and Phi Dihedral Restraints
> To: Brandon Mills <>
> Cc:
> Message-ID: <>
> 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
> --
>              http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 17 Apr 2007 16:49:01 +0800
> From: "" <>
> Subject: [modeller_usage]  using model-loop-refine in Modeller9v1
> To:
> Message-ID: <>
> 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" <>
> Subject: Re: [modeller_usage] using model-loop-refine in Modeller9v1
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> Message-ID: <>
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