Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 39

[Ashish Runthala <ashishr AT bits-pilani.ac.in>]

Dear Knut J,
Please don't use DOPE as such to evaluate model.
NEVER USE DOPE ALONE TO RANK MODELS. ONLY DOPE IS NOT A GOOD SELECTION MEASURE. 
Use normalized_dope or GDT to rank models/Clusters/Hybrid Models.

Ashish



----- Original Message -----
From: "modeller usage-request" <modeller_usage-request AT salilab.org>
To: "modeller usage" <modeller_usage@listsrv.ucsf.edu>
Sent: Monday, February 28, 2011 5:02:41 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 39

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Today's Topics:

   1. Re: Structural alignment	using	iterative_structural_alignment
      (Modeller Caretaker)
   2. about model rank (albert)
   3. Regarding Salign (Ashish Runthala)
   4. Re: about model rank (Knut J Bjuland)


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

Message: 1
Date: Fri, 25 Feb 2011 16:04:47 -0800
From: Modeller Caretaker <modeller-care@ucsf.edu>
Subject: Re: [modeller_usage] Structural alignment	using
	iterative_structural_alignment
To: Seungyeul Yoo <seungyeul.yoo AT mssm.edu>
Cc: modeller_usage@listsrv.ucsf.edu
Message-ID: <4D68439F.3090709 AT salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 2/25/11 9:48 AM, Seungyeul Yoo wrote:
> I was trying to clean two pdb files and superpose them based on the
> pairwise structural alignment.
...
> But when I replaced it to
> 'modeller.salign.iterative_structural_align(aln), I had error message like:

My best guess is that every combination of parameters failed for the 
first loop, so it has no alignment to refine. If you can send me your 
full inputs (which two PDBs are you trying to align?) I'll see if it can 
be fixed.

	Ben Webb, Modeller Caretaker
-- 
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


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

Message: 2
Date: Sun, 27 Feb 2011 23:28:20 +0800 (CST)
From: albert <leuven AT yeah.net>
Subject: [modeller_usage] about model rank
To: modeller_usage <modeller_usage@listsrv.ucsf.edu>
Message-ID: <2e2442cd.2c66.12e67bc0d5d.Coremail.leuven AT yeah.net>
Content-Type: text/plain; charset="gbk"

Hello:
   I've built 1000 models by modeller and I forgot save the log file. So I cannot obtain the DOPE or MOLPDF information for each residues. I am wondering, is it possible to rank then manually?

Thank you very much
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Message: 3
Date: Mon, 28 Feb 2011 16:03:50 +0530 (IST)
From: Ashish Runthala	  <ashishr AT bits-pilani.ac.in>
Subject: [modeller_usage] Regarding Salign
To: modeller <modeller_usage@listsrv.ucsf.edu>
Message-ID:
	<7668023.128551298889230421.JavaMail.root AT mailserver.bits-pilani.ac.in>
	
Content-Type: text/plain; charset=utf-8

Dear Modellers,
How does align2d_mult actually adds the target sequence onto the aligned templates ali file. 
What is the logic considered by align2d_mult to align the target sequence onto the structurally aligned templates' ali file.It just considers topology of coordinates but no structural information is known for target. So how does it considers restraints from templates to align target sequence?

Thanks
Ashish

Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS Pilani
Rajasthan - INDIA



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Message: 4
Date: Mon, 28 Feb 2011 11:32:34 +0100
From: Knut J Bjuland <knutjbj AT hotmail.com>
Subject: Re: [modeller_usage] about model rank
To: modeller_usage@listsrv.ucsf.edu
Message-ID: <4D6B79C2.2060005 AT hotmail.com>
Content-Type: text/plain; charset="x-gbk"

Hi

You can use a script to evaluate dope score for each model you build and 
output the dope score to a log file. Then you can use a spreeadsheet to 
rank the models according to a dope score.

Knut J

Den 27.02.2011 16:28, skrev albert:
> Hello:
> I've built 1000 models by modeller and I forgot save the log file. So 
> I cannot obtain the DOPE or MOLPDF information for each residues. I am 
> wondering, is it possible to rank then manually?
>
> Thank you very much
>
>
> _______________________________________________
> modeller_usage mailing list
> modeller_usage@listsrv.ucsf.edu
> https://salilab.org/mailman/listinfo/modeller_usage

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