Dear Seungyeul Yoo
I surpassed these errors, when you make a script which provides flexibility in optimal iterative alignment for making the maximal possible satisfaction of unaligned segments.
Send me your initial files with the scripts you used. Then i can correct your problems for sure.
Good Luck,
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <modeller_usage-request(a)salilab.org>
To: "modeller usage" <modeller_usage(a)salilab.org>
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
modeller_usage(a)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(a)salilab.org
You can reach the person managing the list at
modeller_usage-owner(a)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: 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(a)salilab.org>
Subject: Re: [modeller_usage] Structural alignment using
iterative_structural_alignment
To: Seungyeul Yoo <seungyeul.yoo(a)mssm.edu>
Cc: modeller_usage(a)salilab.org
Message-ID: <4D68439F.3090709(a)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(a)salilab.org 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(a)yeah.net>
Subject: [modeller_usage] about model rank
To: modeller_usage <modeller_usage(a)salilab.org>
Message-ID: <2e2442cd.2c66.12e67bc0d5d.Coremail.leuven(a)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
