Respected Sir, I tried your approach. It works. But still it wasn't working out the way i want it. Is it possible that you can find the "final max quality" for a model decoy with its native state experimental structure. salign_iterative does work properly for 2 crystal structures but how to make it work for both template/Native State & Model structure.

Thanks, Ashish

----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Saturday, January 22, 2011 2:59:16 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 9

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Today's Topics:

1. Regarding Salign (Ashish Runthala) 2. model_addrsr.py (Koushik A C) 3. Re: model_addrsr.py (Modeller Caretaker) 4. Re: Regarding Salign (Modeller Caretaker)

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Message: 1 Date: Fri, 21 Jan 2011 08:41:47 +0530 (IST) From: Ashish Runthala ashishr@bits-pilani.ac.in Subject: [modeller_usage] Regarding Salign To: modeller modeller_usage@salilab.org Message-ID: 32062261.262361295579507848.JavaMail.root@mailserver.bits-pilani.ac.in Content-Type: text/plain; charset=utf-8

I checked salign too. It considers penalties on primary sequence and then moves to the structural alignment of considered structures before adding target sequence according to generated structural topology. But will you pass me the script lines which aligns structures at 1,2,3,4Angstroms. My another doubt is that how the considered structures are considered all together for each of these distance cutoffs. Is this like nC2 combination based structural alignment satisfaction of restraint matrix generated. Show me where these 1,2,3,4 Angstroms are available in salign_iterative. I couldn't find them.

Thanks, Ashish

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Message: 2 Date: Fri, 21 Jan 2011 13:23:40 +0530 (IST) From: Koushik A C 011113027@sastra.edu Subject: [modeller_usage] model_addrsr.py To: modeller_usage@salilab.org Message-ID: 992863059.70038.1295596420282.JavaMail.root@mail.sastra.edu Content-Type: text/plain; charset="utf-8"

Hi, I am not able to model beta sheets even if i am using model_addrsr,py file. Can anyone please help me out..!!