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
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To: "modeller usage" <>
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)
----------------------------------------------------------------------
Message: 1
Date: Tue, 22 Feb 2011 03:08:12 +0800 (CST)
From: albert <>
Subject: [modeller_usage] bad occupancy from loop refinement
To: modeller_usage <>
Message-ID: <>
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
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Message: 2
Date: Tue, 22 Feb 2011 13:02:59 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] bad occupancy from loop refinement
To: albert <>
Cc: modeller_usage <>
Message-ID: <>
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On 02/21/2011 11:08 AM, albert wrote:
> 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.
It's impossible to tell what your problem is without seeing your input
files.
However, Modeller does not use the occupancy field. If one is present in
your input PDB, it'll leave whatever value is there. If it has to add
atoms, those atoms will be given an occupancy of 1.
Ben Webb, Modeller Caretaker
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------------------------------
Message: 3
Date: Thu, 24 Feb 2011 12:54:33 +0530 (IST)
From: Ashish Runthala <>
Subject: [modeller_usage] Regarding Iterative Sequence Alignment
To: modeller <>
Message-ID:
<>
Content-Type: text/plain; charset=utf-8
Dear Modellers,
I want to generate iterative sequence alignment of Templates before being integrated with the target sequence. How to use salign for optimal iterative alignment only based on sequences, with no consideration of overhang folds.
Thanks
Ashish
Ashish Runthala
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS Pilani,
Rajasthan - INDIA
------------------------------
Message: 4
Date: Thu, 24 Feb 2011 10:31:06 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Regarding Iterative Sequence Alignment
To: Ashish Runthala <>
Cc: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 02/23/2011 11:24 PM, Ashish Runthala wrote:
> I want to generate iterative sequence alignment of Templates before
> being integrated with the target sequence. How to use salign for
> optimal iterative alignment only based on sequences, with no
> consideration of overhang folds.
SALIGN's iterative alignment uses structural information. If you want to
use only sequence information, you could certainly write your own Python
loop to do it. But you'd have to figure out how to determine your
alignment is 'optimal' so you can terminate the loop.
Ben Webb, Modeller Caretaker
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http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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