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: "modeller_usage-request@salilab.org" <modeller_usage-request@salilab.org>
To: modeller_usage@salilab.org
Sent: Tuesday, 10 April 2012 8:58 AM
Subject: modeller_usage Digest, Vol 11, Issue 43

Send modeller_usage mailing list submissions to
    modeller_usage@salilab.org

To subscribe or unsubscribe via the World Wide Web, visit
    https://salilab.org/mailman/listinfo/modeller_usage
or, via email, send a message with subject or body 'help' to
    modeller_usage-request@salilab.org

You can reach the person managing the list at
    modeller_usage-owner@salilab.org

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 <modeller-care@salilab.org>
To: BIN ZHANG <zhngbn@gmail.com>
Cc: modeller_usage@salilab.org
Subject: Re: [modeller_usage] In what are the initial structures
    different?
Message-ID: <4F832E6A.5020001@salilab.org>
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
--
modeller-care@salilab.org            http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


------------------------------

Message: 2
Date: Tue, 10 Apr 2012 08:33:02 +0530 (IST)
From: Ashish Runthala      <ashishr@bits-pilani.ac.in>
To: modeller usage <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
Message-ID:
    <15240798.16751334026982399.JavaMail.root@mailserver.bits-pilani.ac.in>
   
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 <sumedharoy@gmail.com>
To: modeller usage <modeller_usage@salilab.org>
Subject: [modeller_usage] Error in ALIGN_CODES(i)
Message-ID:
    <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=NECA@mail.gmail.com>
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://salilab.org/archives/modeller_usage/attachments/20120409/e4ef0163/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: alignment-ligand.ali
Type: application/octet-stream
Size: 428 bytes
Desc: not available
URL: <http://salilab.org/archives/modeller_usage/attachments/20120409/e4ef0163/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: model-ligand.py
Type: text/x-python
Size: 981 bytes
Desc: not available
URL: <http://salilab.org/archives/modeller_usage/attachments/20120409/e4ef0163/attachment.py>

------------------------------

Message: 3
Date: Mon, 09 Apr 2012 11:44:11 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: Sumedha Roy <sumedharoy@gmail.com>
Cc: modeller usage <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] Error in ALIGN_CODES(i)
Message-ID: <4F832DFB.1020106@salilab.org>
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
--
modeller-care@salilab.org            http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


------------------------------

_______________________________________________
modeller_usage mailing list
modeller_usage@salilab.org
https://salilab.org/mailman/listinfo/modeller_usage


End of modeller_usage Digest, Vol 11, Issue 42
**********************************************


------------------------------

Message: 3
Date: Tue, 10 Apr 2012 08:30:34 +0530 (IST)
From: Ashish Runthala      <ashishr@bits-pilani.ac.in>
To: modeller usage <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
Message-ID:
    <24731645.16721334026834741.JavaMail.root@mailserver.bits-pilani.ac.in>
   
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 <zhngbn@gmail.com>
To: modeller_usage@salilab.org
Subject: [modeller_usage] In what are the initial structures
    different?
Message-ID: <602A5241-132A-4319-81BA-94C238A459AF@gmail.com>
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


------------------------------

_______________________________________________
modeller_usage mailing list
modeller_usage@salilab.org
https://salilab.org/mailman/listinfo/modeller_usage


End of modeller_usage Digest, Vol 11, Issue 43
**********************************************