Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 83

[Ashish Runthala <ashishr AT bits-pilani.ac.in>]

Dear James,
You search for Salign_*.py scripts in MODELLER and then you can integrate both the templates. However, you need to include both the template to later curate the alignment file as per your  fusion consideration requirement. 

Regards
Ashish

Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA

----- Original Message -----
From: "modeller usage-request" <modeller_usage-request AT salilab.org>
To: "modeller usage" <modeller_usage@listsrv.ucsf.edu>
Sent: Wednesday, 8 August, 2012 18:57:12 GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 11, Issue 83

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Today's Topics:

   1. Re: struggling to make structure predictions (Modeller Caretaker)
   2. Template PDB files (Nanda Pandey)
   3. Re: Template PDB files (Modeller Caretaker)
   4. Modelling of Chimeric protein (James Starlight)


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Message: 1
Date: Mon, 06 Aug 2012 18:22:09 -0700
From: Modeller Caretaker <modeller-care@ucsf.edu>
To: "Adhikari, Badri (MU-Student)" <bap54 AT mail.missouri.edu>
Cc: "modeller_usage@listsrv.ucsf.edu" <modeller_usage@listsrv.ucsf.edu>
Subject: Re: [modeller_usage] struggling to make structure predictions
Message-ID: <50206DC1.10905 AT salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 8/6/12 2:24 PM, Adhikari, Badri (MU-Student) wrote:
> I am struggling to write a python program that takes protein sequence as
> input and produces some conformations as the output (with no any other
> input data).

The scripts you've attached are IMP scripts. This is the Modeller 
mailing list. You'd probably have more luck on the IMP mailing list.

	Ben Webb, Modeller Caretaker
-- 
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


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Message: 2
Date: Tue, 7 Aug 2012 17:38:21 +0530
From: Nanda Pandey <pnanda1780 AT gmail.com>
To: modeller_usage@listsrv.ucsf.edu
Subject: [modeller_usage] Template PDB files
Message-ID:
	<CAPR-BHD352XAOK_w-k2aia7wyN+N8_z5q=vS_NhxYVVPDzTsOQ AT mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

I am very new to modeller so a small query, Please let me know how do I
compare the template sequences using compare script. Do I need to download
individual template files from PDB or Is there any other possible way.
Also, whta should be done in case I have too many template sequences with
same e -value (e.g. 0 e -value) should i download all of them??

Thanks and Regards.
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Message: 3
Date: Tue, 07 Aug 2012 09:16:12 -0700
From: Modeller Caretaker <modeller-care@ucsf.edu>
To: Nanda Pandey <pnanda1780 AT gmail.com>
Cc: modeller_usage@listsrv.ucsf.edu
Subject: Re: [modeller_usage] Template PDB files
Message-ID: <50213F4C.9050407 AT salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 8/7/12 5:08 AM, Nanda Pandey wrote:
> I am very new to modeller so a small query, Please let me know how do I
> compare the template sequences using compare script. Do I need to
> download individual template files from PDB

Yes, you will need to download template PDB files.

> Also, whta should be done in case I have too many template
> sequences with same e -value (e.g. 0 e -value) should i download all of
> them??

You can if you like - how you choose which template(s) to use for 
modeling is up to you.

	Ben Webb, Modeller Caretaker
-- 
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


------------------------------

Message: 4
Date: Wed, 8 Aug 2012 06:27:10 -0700
From: James Starlight <jmsstarlight AT gmail.com>
To: modeller_usage@listsrv.ucsf.edu
Subject: [modeller_usage] Modelling of Chimeric protein
Message-ID:
	<CAALQopxSJGmtJAF9s-DyJG78X1JJ1vy-63fARNpBCktgEvKJEA AT mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear Modeller's users!

I want to model chimeric protein which consist of two fussed proteins
( tail to head fussion C to N termi). It's important that both of that
proteins have known spatial structures which could be used as the
templates.

In the input I can define merged sequences of my proteins as one entry.
Is there any way to use both of the templates to guide such modelling
? In the input option I've found only possibility to use one template.
What extra additions should I provide for better modelling of the
fussed protein?

Thanks for help

Gleb


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