Script is wrong,
Use knowns='5fd1A' (with ChainID) because this is a protein.
For ligand bound residue put a . in the alignment file, so that MODELLER can include the attached ligand too in the model.
Then it will correctly call
assess_methods=(assess.DOPE, assess.GA341)) (Last line of your initial set of lines).
If you are using 5FD1 as the PDB file to model your sequence 1fdx, then you should definitely have the DOPE Score calculated.
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <>
To: "modeller usage" <>
Sent: Tuesday, April 10, 2012 11:12:30 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 11, Issue 44
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Today's Topics:
1. Re: modeller_usage Digest, Vol 11, Issue 42 (Modeller Caretaker)
2. calculating DOPE score (NUTAN CHAUHAN)
----------------------------------------------------------------------
Message: 1
Date: Mon, 09 Apr 2012 20:35:37 -0700
From: Modeller Caretaker <>
To: Ashish Runthala <>
Cc: modeller usage <>
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 4/9/12 8:00 PM, Ashish Runthala wrote:
> MODELLER based on your constructed alignment file
> parsing the reliable template residues mapped against the target
> ones, constructs and fixes the average alpha carbon backbone
Actually all atoms that have the same name in target and template will
be simply copied into the model in this case. Usually this means all
backbone atoms, not just alpha carbons.
> On increased sampling,
> MODELLER tries best to satisfy the Lennard Jones and all the
> energetic equations composing its DOPE energy function.
In fact the optimization tries to minimize the molecular PDF, which
includes contributions from soft sphere (not Lennard Jones). DOPE is a
separate, atomistic pairwise statistical potential. It is not used in
comparative modeling.
Ben Webb, Modeller Caretaker
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http://www.salilab.org/modeller/
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Message: 2
Date: Tue, 10 Apr 2012 13:29:27 +0800 (SGT)
From: NUTAN CHAUHAN <>
To: "" <>
Subject: [modeller_usage] calculating DOPE score
Message-ID:
<>
Content-Type: text/plain; charset="iso-8859-1"
Hello all,
I am trying to build a protein-ligand model using align-ligand.ali file. . Below is ?the python script to generate 5 model and to ?calculate the Dope and GA score.?but I am unable to calculate the DOPE score and GA score. Plz help
from modeller import *
from modeller.automodel import *
log.verbose() ? ?# request verbose output
env = environ() ?# create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
env = environ()
a = automodel(env, alnfile='alignment.ali',
? ? ? ? ? ? ? knowns='5fd1', sequence='1fdx',
? ? ? ? ? ? ? assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 5
a.make()
?
Regards,
Nutan Chauhan
Research Scholar
Department of Biotechnology
BIT, Mesra
Ranchi-835215, Jharkhand
________________________________
From: "" <>
To:
Sent: Tuesday, 10 April 2012 8:58 AM
Subject: modeller_usage Digest, Vol 11, Issue 43
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???
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??? https://salilab.org/mailman/listinfo/modeller_usage
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???
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???
When replying, please edit your Subject line so it is more specific
than "Re: Contents of modeller_usage digest..."
Today's Topics:
? 1. Re: In what are the initial structures different?
? ? ? (Modeller Caretaker)
? 2. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala)
? 3. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala)
----------------------------------------------------------------------
Message: 1
Date: Mon, 09 Apr 2012 11:46:02 -0700
From: Modeller Caretaker <>
To: BIN ZHANG <>
Cc:
Subject: Re: [modeller_usage] In what are the initial structures
??? different?
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 04/08/2012 11:58 PM, BIN ZHANG wrote:
> I have a question about the differences of the initial structure built
> for homology modeling. Can anyone tell me how exactly are these initial
> structures different? Do they differ in the secondary structures in
> uncertain regions? I cannot find this information in the manual.
See http://salilab.org/modeller/9.10/manual/node470.html, in particular
step 3 and substep 3. The initial structures are simply randomized by
calling selection.randomize_xyz().
??? Ben Webb, Modeller Caretaker
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? ? ? ? ? ? http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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Message: 2
Date: Tue, 10 Apr 2012 08:33:02 +0530 (IST)
From: Ashish Runthala??? ? <>
To: modeller usage <>
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
Message-ID:
??? <>
???
Content-Type: text/plain; charset=utf-8
Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file.
So it could probably be '2AHNA' or '2AHNB'.
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
------------------------------
Message: 2
Date: Mon, 9 Apr 2012 17:21:12 +0530
From: Sumedha Roy <>
To: modeller usage <>
Subject: [modeller_usage] Error in ALIGN_CODES(i)
Message-ID:
??? <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=>
Content-Type: text/plain; charset="iso-8859-1"
Hello all,
When I try to model my protein-DNA complex, I get the error:
_modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i)
was not found in the alignment file; ALIGN_CODES(? ? ? 2) =? 2AHN
But I see no mistake either in the alignment or the format. I've attached
both the ALI file and model-ligand.py. Please help!!!
--
Sumedha Roy
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------------------------------
Message: 3
Date: Mon, 09 Apr 2012 11:44:11 -0700
From: Modeller Caretaker <>
To: Sumedha Roy <>
Cc: modeller usage <>
Subject: Re: [modeller_usage] Error in ALIGN_CODES(i)
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 04/09/2012 04:51 AM, Sumedha Roy wrote:
> When I try to model my protein-DNA complex, I get the error:
> _modeller.ModellerError: read_al_373E> Protein specified in
> ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(
> 2) =? 2AHN
>
> But I see no mistake either in the alignment or the format. I've
> attached both the ALI file and model-ligand.py. Please help!!!
Your alignment file is in incorrect format. Each sequence must start
with a >P1; header. Your second sequence starts with >P2; instead.
??? Ben Webb, Modeller Caretaker
--
? ? ? ? ? ? http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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------------------------------
Message: 3
Date: Tue, 10 Apr 2012 08:30:34 +0530 (IST)
From: Ashish Runthala??? ? <>
To: modeller usage <>
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
Message-ID:
??? <>
???
Content-Type: text/plain; charset=utf-8
Dear? BIN ZHANG,
MODELLER based on your constructed alignment file parsing the reliable template residues mapped against the target ones, constructs and fixes the average alpha carbon backbone (if you choose a single template) or an average backbone topology (for Multiple templates' local aligned chunks). Then it fits in the side chains and backbone atoms to make the model complete.?
However, easy saying but really a vicious circle problem, the alignment could have actually been wrong to incorrectly fit target against parsed template residues.
Regardless of the earlier problems, On increased sampling, MODELLER tries best to satisfy the Lennard Jones and all the energetic equations composing its DOPE energy function. The non-physical local atomic clashes are thus minimized with every such iteration. So only you see, Restraints earlier, now with end of every such iterative step. That in fact, is the trial to leap the energetic landscape, precisely focusing on the probably erroneous regions encompassing the higher local steric clashes.
The story continues until the number of iterations are over.
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
Message: 1
Date: Sun, 8 Apr 2012 23:58:13 -0700
From: BIN ZHANG <>
To:
Subject: [modeller_usage] In what are the initial structures
??? different?
Message-ID: <>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Dear All:
I have a question about the differences of the initial structure built?
for homology modeling. Can anyone tell me how exactly are these?
initial structures different? Do they differ in the secondary?
structures in uncertain regions? I cannot find this information in the?
manual.
For example, by using
a = automodel()
a.starting_model = 1
a.ending_model = 50
I can built 50 different homology models starting from different?
initial structures, but I have want to know how these different?
initial structures are constructed.
Thanks very much for help.
Best,
Bin
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