Hi Benn, Check it out. I want to consider maximal/average occupancy of a residue at a position to select the better possible residue conformation, augmenting the overall accuracy of the model.

Tell me a way to consider all templates in a script, develop iterative optimal alignment based only on sequence, i.e. without your RMS or cutoff thresholds for superimpositions. This alignment considers maximal propensity of a residue at every location, among available residues of considered templates, and put gaps for others at same locus in the alignment file for other templates.

Thanks Ashish

----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Friday, February 25, 2011 12:01:29 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 37

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Today's Topics:

1. bad occupancy from loop refinement (albert) 2. Re: bad occupancy from loop refinement (Modeller Caretaker) 3. Regarding Iterative Sequence Alignment (Ashish Runthala) 4. Re: Regarding Iterative Sequence Alignment (Modeller Caretaker)

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Message: 1 Date: Tue, 22 Feb 2011 03:08:12 +0800 (CST) From: albert leuven@yeah.net Subject: [modeller_usage] bad occupancy from loop refinement To: modeller_usage modeller_usage@salilab.org Message-ID: 7f59a41d.528d.12e499f311b.Coremail.leuven@yeah.net Content-Type: text/plain; charset="gbk"

Hello: I am using loop refinement protocol based on known PDB file method for loop refinement. What surprised me is that: the occupancy for each atom in the refined structure is more than 1. here is some list, can you tell me why?

THX

-----------------------------Loop refinement---------------------------------------------- EXPDTA THEORETICAL MODEL, MODELLER 9v8 2011/02/18 21:54:47 REMARK 6 MODELLER OBJECTIVE FUNCTION: -11.8879 ATOM 1 N SER A 1 53.405 4.206 73.937 59.86 59.86 ATOM 2 CA SER A 1 54.091 5.156 73.036 59.86 59.86 ATOM 3 CB SER A 1 53.358 5.255 71.687 59.86 59.86 ATOM 4 OG SER A 1 53.443 4.020 70.992 59.86 59.86 ATOM 5 C SER A 1 54.148 6.519 73.639 59.86 59.86 ATOM 6 O SER A 1 54.469 6.679 74.816 59.86 59.86 ATOM 7 N ALA A 2 53.848 7.547 72.824 39.90 39.90 ATOM 8 CA ALA A 2 53.862 8.892 73.313 39.90 39.90