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
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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 <>
Subject: [modeller_usage] Regarding Salign
To: modeller <>
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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 <>
Subject: [modeller_usage] model_addrsr.py
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Hi, I am not able to model beta sheets even if i am using model_addrsr,py file. Can anyone please help me out..!!
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Message: 3
Date: Fri, 21 Jan 2011 13:20:02 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] model_addrsr.py
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On 1/20/11 11:53 PM, Koushik A C wrote:
> Hi, I am not able to model beta sheets even if i am using
> model_addrsr,py file. Can anyone please help me out..!!
Please post your script file so we can see where your problem is.
Ben Webb, Modeller Caretaker
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Message: 4
Date: Fri, 21 Jan 2011 13:29:04 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Regarding Salign
To: Ashish Runthala <>
Cc: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 1/20/11 7:11 PM, Ashish Runthala wrote:
> 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.
This is not how salign functions in general, but this is basically how
the iterative_structural_align() method functions. It uses an
SALIGN-generated sequence alignment as the starting point for a
structural alignment.
> But will you pass me the script lines which aligns
> structures at 1,2,3,4Angstroms.
You can generate a quality score at any cutoff you desire. Set
output='QUALITY' and rms_cutoff to the desired cutoff. For the
iterative_structural_align() a cutoff of 3.5A is used.
Ben Webb, Modeller Caretaker
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