Respected Sir Benn,
You didn't tell me the Alignment Score formula. Please share that. And you didn't tell me the utility of such a score, which looses its significance mostly, without being parallel to correct template selection/Model Accuracy.
Thanks
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
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To: "modeller usage" <>
Sent: Wednesday, April 13, 2011 8:26:21 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 69
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Today's Topics:
1. Re: How Alignment Score is calculated. (Modeller Caretaker)
2. modifiable version of salign.iterative_structural_align()
(Benjamin SCHWARZ)
3. Re: modifiable version of salign.iterative_structural_align()
(Modeller Caretaker)
4. Modelling a protein loop close to DNA ..... (Sergio Garay)
----------------------------------------------------------------------
Message: 1
Date: Mon, 11 Apr 2011 10:16:57 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] How Alignment Score is calculated.
To: Ashish Runthala <>
Cc: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 04/09/2011 10:00 PM, Ashish Runthala wrote:
> When pairwise alignment score calculated by MODELLER
> is not parallel to the Model Accuracy. Then what is the benefit
> Alignment Score holds for? Benn, will you please tell me the formula
> for calculating Alignment Score for a pairwise alignment. What is the
> matrix it uses for alignment and score computation. How it is
> calculated.
The alignment score is simply the sum of residue-residue distances and
gap penalties from tracing the path that dynamic programming finds
through the alignment matrix.
In general, alignment scores are a poor predictor of model quality. I'm
not aware of any claims to the contrary in the Modeller documentation.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 2
Date: Tue, 12 Apr 2011 16:27:40 +0200
From: Benjamin SCHWARZ <>
Subject: [modeller_usage] modifiable version of
salign.iterative_structural_align()
To: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=us-ascii
Hi list,
If I understand well, the salign.iterative_structural_align() function is an exact implementation of the algorithm presented in [Madhusudhan2009]. Is there a python script version of this function ? Something that could be tweaked and modified...
--Ben.S
------------------------------
Message: 3
Date: Tue, 12 Apr 2011 09:11:00 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] modifiable version of
salign.iterative_structural_align()
To: Benjamin SCHWARZ <>
Cc: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 4/12/11 7:27 AM, Benjamin SCHWARZ wrote:
> If I understand well, the salign.iterative_structural_align()
> function is an exact implementation of the algorithm presented in
> [Madhusudhan2009]. Is there a python script version of this function
> ? Something that could be tweaked and modified...
Of course - all the Modeller scripts are Python scripts, so you can
modify them to your heart's content. Look at modlib/modeller/salign.py.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 4
Date: Wed, 13 Apr 2011 07:09:59 -0400
From: Sergio Garay <>
Subject: [modeller_usage] Modelling a protein loop close to DNA .....
To:
Message-ID: <BANLkTimgaTV=x3+>
Content-Type: text/plain; charset="iso-8859-1"
Hi all
I have obtained a reasonably good model of protein dimer close to a DNA
molecule just copying the DNA template into my target. But now I want to
refine a protein loop close to DNA molecule but taking into account all
"real" interactions between the atoms of my protein and DNA. At the moment I
was not able to make modeller to recognize my target dna bases. So, my
question is: if the ordering of the DNA base atoms in my pdb record are
different to the one in top_heav.lib, Should I change it in my pdb or Should
I rewrite the top in order to it matches with that of pdb file. Which method
would be easier? . Below I paste a desoxi Gua from top_heav.lib (left) and a
Gua residue from my template pdb in order to show the differences (right):
RESI DGUA -1.00000
ATOM P P 1.50000 // ATOM 37 P DG A
3 49.258 12.669 8.835
ATOM OP1 ON3 -0.80000 // ATOM 38 OP1 DG A 3 48.625
13.322 7.669
ATOM OP2 ON3 -0.80000 // ATOM 39 OP2 DG A 3 49.792
11.303 8.659
ATOM O5' ON2 -0.55000 // ATOM 40 O5' DG A 3
50.393 13.597 9.434
ATOM C5' CN8 0.10000 // ATOM 41 C5' DG A 3
50.007 14.836 10.056
ATOM C4' CN6 0.20000 // ATOM 42 C4' DG A 3
50.897 15.123 11.268
ATOM O4' ON6 -0.40000 // ATOM 43 O4' DG A 3
50.655 14.196 12.319
ATOM C1' CN6B 0.20000 // ATOM 44 C3' DG A 3
52.366 15.009 10.907
ATOM N9 NN2 -0.14000 // ATOM 45 O3' DG A 3
53.017 15.983 11.686
ATOM C4 CN5 0.14000 // ATOM 46 C2' DG A 3
52.724 13.583 11.293
ATOM N3 NN3A -0.66000 // ATOM 47 C1' DG A 3
51.785 13.331 12.470
ATOM C2 CN2 0.76000 // ATOM 48 N9 DG A 3
51.356 11.909 12.533
ATOM N1 NN2G -0.10000 // ATOM 49 C4 DG A 3 51.166
11.181 13.676
ATOM N2 NN1 0.00000 // ATOM 50 C8 DG A 3
51.170 11.020 11.508
ATOM C6 CN1 0.55000 // ATOM 51 N7 DG A 3
50.833 9.812 11.874
ATOM O6 ON1 -0.47000 // ATOM 52 C5 DG A 3
50.777 9.903 13.268
ATOM C5 CN5 -0.08000 // ATOM 53 C6 DG A 3
50.374 8.977 14.276
ATOM N7 NN4 -0.69000 // ATOM 54 O6 DG A 3
49.799 7.879 14.135
ATOM C8 CN4 0.69000 // ATOM 55 N1 DG A 3
50.574 9.420 15.560
ATOM C2' CN6C 0.00000 // ATOM 56 C2 DG A 3 51.068
10.663 15.839
ATOM C3' CN6 0.10000 // ATOM 57 N3 DG A 3 51.310
11.614 14.951
ATOM O3' ON2 -0.55000 // ATOM 58 N2 DG A 3 51.319
10.942 17.075
I also changed my alignment in order to the bases can be recognized:
>P1; TCP16
sequence:TCP16:::::::0.00:0.00
tjltllljjjejle
/
tjltllljjjejle
/
TPKDRHLKIGGRDRRIRI-----PPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA
ATGHG
/
TPKDRHLKIGGRDRRIRI-----PPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA
ATGHG
*
>P1; TCP16
structureX:TCP16:1:A:148:D:::-1.00:-1.00
tjltllljjjejle
/
tjltllljjjejle
/
TPKDRHLKIGGRD-----RRIRIPPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA
ATGHG
/
TPKDRHLKIGGRD-----RRIRIPPSVAPQLFRLTKELGFKTDGETVSWLLQNAEPAIFA
ATGHG
*
Below I also paste the python script that I've used in the modelling. May be
someone can find any error o misleading command.
# Loop refinement of an existing model
from modeller import *
from modeller.automodel import *
log.verbose()
env = environ()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
#env.io.hetatm = True
# Create a new class based on 'loopmodel' so that we can redefine
# select_loop_atoms (necessary)
class MyLoop(loopmodel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms
rsr.add(forms.gaussian(group=physical.xy_distance,
feature=features.distance(at['CZ:45:C'],
at['O6:6:A']),
mean=3.0, stdev=0.5))
rsr.add(forms.gaussian(group=physical.xy_distance,
feature=features.distance(at['CZ:105:D'],
at['O6:20:B']),
mean=3.0, stdev=0.5))
# This routine picks the residues to be refined by loop modeling
#def special_restraints(self, aln):
def select_loop_atoms(self):
#Two loops for refinement at the same time
return selection(self.residue_range('44:C', '47:C'),
self.residue_range('103:D', '106:D'))
m = MyLoop(env,
alnfile = 'align2.ali' ,
inimodel='TCP16.B99990001.pdb', # initial model of the target
sequence='TCP16') # code of the target
m.loop.starting_model= 1 # index of the first loop model
m.loop.ending_model = 1 # index of the last loop model
m.loop.md_level = refine.very_slow # loop refinement method
m.make()
Any help or advice will be very appreciated.
Sergio
--
Sergio Garay
Dr. en Ciencias Biol?gicas
Facultad de Bioquimica y Cs. Biol?gicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221
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