As Webb has told. Follow that and you may use these to get good models.
1. Generate maximum possible model number.
2. Try to look for multiple templates for your target sequence.
3. Try to see the alignment file, if your model lacks the conserved sequence information somewhere resulting in complete loss of fold, locally at some place.
4. Try to assess models with all the means provided and then select the best model. Don't rely on any single assessment test.
5. Refinement is not of any usage if you are trapped in local minima earlier in the Potential Energy Surface topological curve.
Good Luck,
Ashish
----- Original Message -----
From: "modeller usage-request" modeller_usage-request@salilab.org
To: "modeller usage" modeller_usage@salilab.org
Sent: Tuesday, May 11, 2010 7:37:36 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 9, Issue 74
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Today's Topics:
1. Re: How to optimize a Homology model. (Modeller Caretaker)
2. How to generate Homology models using a computer farm
(Caio Veloso)
3. Re: How to generate Homology models using a computer farm
(Modeller Caretaker)
4. how to extract the part of structure from a complex ? (Yue)
----------------------------------------------------------------------
Message: 1
Date: Mon, 10 May 2010 07:46:44 -0700
From: Modeller Caretaker modeller-care@salilab.org
Subject: Re: [modeller_usage] How to optimize a Homology model.
To: Harish Reddy harisredy@gmail.com
Cc: modeller_usage@salilab.org
Message-ID: 4BE81C54.9020405@salilab.org
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/7/10 7:42 PM, Harish Reddy wrote:
> I need some help with optimization. I am confused what to do.
Your best option is to build more models, assess them, and choose the
best one (or change your alignment/template if none of the models are
acceptable). You would be better off doing this with Python scripts, as
the old Modeller TOP scripts are no longer documented or supported.
> On the first instance i used the scrip one to build the models. As i was
> not satisfied with the structural quality of the models, i used the
> second script below where i included a refinement command. Even then i
> couldn't get good models. So, i tried to a optimization script (third)
Actually, all your scripts do the same thing - they call the regular
modeling procedure. You have changed the amount of refinement and the
optimization parameters slightly, but this does not usually have a large
influence on the output models.
> But that
> script just kept on failing. So, I am not sure what the problem is..
I can't tell what the problem is either! What do you mean by "the script
just kept on failing" ?
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: Mon, 10 May 2010 17:19:16 -0300
From: Caio Veloso
caju@uai.com.br
Subject: [modeller_usage] How to generate Homology models using a
computer farm
To: modeller_usage@salilab.org
Message-ID:
4BE86A44.5000807@uai.com.br
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear All,
In order to build several models of a target protein, we are running
the same Python script on different computers at the same time.
In this case, the script is the same and the proteins used as models
are also the same.
At the first attempt we expected to build different models and then
assess them, and choose the
best one or change your alignment/template if none of the models are
acceptable.
However when these models were evaluated, we discovered that MODELLER
has built
the same models, in the same order on all computers.
I want know whether exist some parameters that could be adjusted at the
Python script,
(a kind of random number generator ?) in order to assure that different
sets of models
will be generate on each computer?
Regards,
Caio Veloso
------------------------------
Message: 3
Date: Mon, 10 May 2010 14:29:25 -0700
From: Modeller Caretaker
modeller-care@salilab.org
Subject: Re: [modeller_usage] How to generate Homology models using a
computer farm
To: Caio Veloso
caju@uai.com.br
Cc: modeller_usage@salilab.org
Message-ID:
4BE87AB5.7090104@salilab.org
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/10/10 1:19 PM, Caio Veloso wrote:
> In order to build several models of a target protein, we are running
> the same Python script on different computers at the same time.
...
> we discovered that MODELLER has built the same models, in the same
> order on all computers.
Indeed, because Modeller is deterministic, and gives reproducable results.
> I want know whether exist some parameters that could be adjusted at
> the Python script, (a kind of random number generator ?) in order to
> assure that different sets of models will be generate on each
> computer?
You need to set rand_seed to a different value on each machine -
something like -2 - (number of machine) should do the trick:
http://salilab.org/modeller/9v8/manual/node110.html
Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org
http://www.salilab.org/modeller/
Modeller mail list:
http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 4
Date: Tue, 11 May 2010 09:54:33 +0800 (CST)
From: Yue
coolmoon@yahoo.cn
Subject: [modeller_usage] how to extract the part of structure from a
complex ?
To: modeller_usage@salilab.org
Message-ID:
11138.10742.qm@web92402.mail.cnh.yahoo.com
Content-Type: text/plain; charset="iso-8859-1"
Hi, everybody
?I have a? question, how to extract a ligand-part fragment of protein (mainly is catalyzed domain) in PDB format?? e.g. in advaced example(), how? to get the 1emd_bs from 1emd.pdb?
?I tried to text editor to edit the part, but i failed.
?Thanks for any advise!
?????????????????????????????????????????????????????????????????????????????????????????????????????????? YJ
?
?
