Dear Lin,
I wrote a script in C to do all that. You can use it to do the analysis for specific chains. You can even do the analysis for specific segment of residues in a specific chain.
If you want, I will provide you the help by providing the binary.
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
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To: "modeller usage" <>
Sent: Friday, April 1, 2011 10:01:26 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 59
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Today's Topics:
1. unsubscribing (Bo Yang)
2. salign: specify chains to superpose (Yingjie Lin)
3. salign: specify chains to superpose (Yingjie Lin)
4. Are gap in target and template same. (Ashish Runthala)
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Message: 1
Date: Thu, 31 Mar 2011 08:07:11 -0700 (PDT)
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unsubscribing
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Message: 2
Date: Thu, 31 Mar 2011 12:08:41 -0400
From: Yingjie Lin <>
Subject: [modeller_usage] salign: specify chains to superpose
To: modeller <>
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Hi Modellers,
I wonder what is the best way to superpose two multi-chain proteins, and explicitly specify the chains to include in superposition. I know that I can read only the wanted chains into the alignment, but I also want to make sure that the other chains move according to the superposition.
Here are two ways we could think of:
1. read only the wanted chains and do superposition.
Then move the other chains accordingly using functions like selection.rotate_origin(), selection.rotate_mass_center() and selection.transform().
2.
model1 <= all chains in protein A
model2 <= all chains in protein B
model3 <= the chain(s) selected for superposition in protein B
first, superpose model3 to model1 (model3 is moved)
second, superpose model2 to model3 (model2 is moved)
Are there any better ways? Thank you.
Yingjie
------------------------------
Message: 3
Date: Thu, 31 Mar 2011 13:50:37 -0400
From: Yingjie Lin <>
Subject: [modeller_usage] salign: specify chains to superpose
To: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=us-ascii
Hi Modellers,
I wonder what is the best way to superpose two multi-chain proteins, and explicitly specify the chains to include in superposition. I know that I can read only the wanted chains into the alignment, but I also want to make sure that the other chains move according to the superposition.
Here are two ways we could think of:
1. read only the wanted chains and do superposition.
Then move the other chains accordingly using functions like selection.rotate_origin(), selection.rotate_mass_center() and selection.transform().
2.
model1 <= all chains in protein A
model2 <= all chains in protein B
model3 <= the chain(s) selected for superposition in protein B
first, superpose model3 to model1 (model3 is moved)
second, superpose model2 to model3 (model2 is moved)
Are there any better ways? Thank you.
Yingjie
------------------------------
Message: 4
Date: Fri, 1 Apr 2011 09:57:47 +0530 (IST)
From: Ashish Runthala <>
Subject: [modeller_usage] Are gap in target and template same.
To: modeller <>
Message-ID:
<>
Content-Type: text/plain; charset=utf-8
Dear Modellers,
I am facing an interesting problem. Are gaps in target and template same, as shown below.
Target AAAAA AA--A AA--A
Template AA--A AAAAA AA--A
CaseI CaseII CaseIII
Are these three cases I,II, & III modelled the same way. How will the gap penalties be incorporated in these three cases, when the modeller calculates the alignment score.
PLEASE PROVIDE ME COMPLETE DETAILS ABOUT GAP PENALTIES IN THESE THREE CASES.
Thanks
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
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