Dear SCHWARZ,
Salign alterations won't help much, as such all the times. Some improvements in TBM-HA modeling can be achieved with some alteration of few parameters as the best set applied, over the default MODELLER set of parameters, and that too only when you have enough coordinate information available for a target sequence. But if you think to change (heartly as Benn said), think of augmented improvement of each parameter with the another alteration.
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/
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------------------------------
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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