Dear Modellers, Whenever the SAlign is implemented with a set of templates, it generates a matrix showing some mutual similarity of templates (pairwise equivalences), something like this (against the target with 326 residues).

1SMQA 1H0OA 1SMQA 0 168 1H0OA 0 0

Now, answer me a set of queries. 1. Is 168 showing the count of similar residues, falling within the specified RMSD threshold? 2. Is this calculation considering LGA algorithm? 3. As there are certain folds existing in every such alignment, is there any lower limit of the existing residues in every such chunk to be considered similar. Like, if a fold is more than 3 residues long, i will take it similar in the matrix, and thus i would leave all the nuclear aligned residues. Is it considered this way in the program?

Best, 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: Tuesday, November 20, 2012 9:54:46 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 109

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1. Re: Modeller Help (Modeller Caretaker) 2. optimization protocol and HETATM flexibility (sdimicco) 3. Error while running compare.py (Anogna)

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Message: 1 Date: Mon, 19 Nov 2012 13:15:30 -0800 From: Modeller Caretaker modeller-care@salilab.org To: mario rossi sanzodenzel@yahoo.it Cc: "modeller_usage@salilab.org" modeller_usage@salilab.org Subject: Re: [modeller_usage] Modeller Help Message-ID: 50AAA172.6070202@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 11/19/2012 05:59 AM, mario rossi wrote: > I'am Simone an italian student, ineed to learn to use modeller to do > homology modelingbut i have some trouble. > I downloaded and installed both modeller and python on my pc (windows > 7). To learn what to do I tried to follow the basic tutorial but I find > serious problems in giving the input. I can not even load the sequence > as the file (.ali) is not recognized by python and if the command is > entered manually, I get syntax error?? Can you help me to understand > where is the mistake?

It's difficult to know what the problem is without a clearer description of what you did, and what results you got.

Ben Webb, Modeller Caretaker