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@salilab.org To: "modeller usage" modeller_usage@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

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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)

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Message: 1 Date: Fri, 25 Feb 2011 16:04:47 -0800 From: Modeller Caretaker modeller-care@salilab.org Subject: Re: [modeller_usage] Structural alignment using iterative_structural_alignment To: Seungyeul Yoo seungyeul.yoo@mssm.edu Cc: modeller_usage@salilab.org Message-ID: 4D68439F.3090709@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