Dear Ramana, There is a script optimize.py. But MD+SA is already working. You won't get contrasting significant better model decoy. Run MODELLER for longer run to select decoy as per 3D-Jury or any other clustering method.

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: Wednesday, April 20, 2011 2:50:13 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 73

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Today's Topics:

1. Re: Long loop modeling (bharat lal) 2. restrict salign to subparts of some structures sequences (Benjamin SCHWARZ) 3. How to run flexEM package parallel (ruiz@berkeley.edu) 4. (no subject) (rjayashree13-science@yahoo.co.in)

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Message: 1 Date: Fri, 15 Apr 2011 19:06:26 +0530 (IST) From: bharat lal monu46010@yahoo.com Subject: Re: [modeller_usage] Long loop modeling To: modeller modeller_usage@salilab.org Message-ID: 650005.60727.qm@web94712.mail.in2.yahoo.com Content-Type: text/plain; charset="iso-8859-1"

Hi,

I want ?to know whether long loop modeling of 30 or 40 residue length is possible through modeller or not ??..

----------? Bharat