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" <>
To: "modeller usage" <>
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
Send modeller_usage mailing list submissions to
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
You can reach the person managing the list at
When replying, please edit your Subject line so it is more specific
than "Re: Contents of modeller_usage digest..."
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 <>
Subject: Re: [modeller_usage] Structural alignment using
iterative_structural_alignment
To: Seungyeul Yoo <>
Cc:
Message-ID: <>
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
--
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 <>
Subject: [modeller_usage] about model rank
To: modeller_usage <>
Message-ID: <>
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://salilab.org/archives/modeller_usage/attachments/20110227/81097b68/attachment.html
------------------------------
Message: 3
Date: Mon, 28 Feb 2011 16:03:50 +0530 (IST)
From: Ashish Runthala <>
Subject: [modeller_usage] Regarding Salign
To: modeller <>
Message-ID:
<>
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
------------------------------
Message: 4
Date: Mon, 28 Feb 2011 11:32:34 +0100
From: Knut J Bjuland <>
Subject: Re: [modeller_usage] about model rank
To:
Message-ID: <>
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
>
> https://salilab.org/mailman/listinfo/modeller_usage
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://salilab.org/archives/modeller_usage/attachments/20110228/b810859f/attachment.html
------------------------------
_______________________________________________
modeller_usage mailing list
https://salilab.org/mailman/listinfo/modeller_usage
End of modeller_usage Digest, Vol 10, Issue 39
**********************************************