Hello all, I want to model my protein using template with its ligand bound to it. How can do this..i dnt hv idea. plz help. thnx in advance, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand
________________________________ From: "modeller_usage-request@salilab.org" modeller_usage-request@salilab.org To: modeller_usage@salilab.org Sent: Saturday, 24 March 2012 10:27 PM Subject: modeller_usage Digest, Vol 11, Issue 34
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Today's Topics:
1. Re: Is it possible to calculate energy for the given structure with MODELLER's C API and derivative with respect to all coordinates (x, y, z)? (Modeller Caretaker) 2. Re: homology modelling with multiple subunits (Modeller Caretaker) 3. Regarding protein 3D structure modeling (vishal Nemaysh) 4. Re: Regarding protein 3D structure modeling (Modeller Caretaker)
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Message: 1 Date: Thu, 22 Mar 2012 13:44:59 -0700 From: Modeller Caretaker modeller-care@salilab.org To: Valerio Lupperger valerio.lupperger@gmx.net Cc: modeller_usage@salilab.org Subject: Re: [modeller_usage] Is it possible to calculate energy for the given structure with MODELLER's C API and derivative with respect to all coordinates (x, y, z)? Message-ID: 4F6B8F4B.6020705@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 3/22/12 8:08 AM, Valerio Lupperger wrote: > I use MODELLER (9.10) in a c-program like in > http://salilab.org/modeller/manual/node456.html. As input I have one > structure and its restraints. Is it possible to calculate energy for the > given structure with MODELLER's C API and derivative with respect to all > coordinates (x,y,z)? And if so, how is it possible?
If you can do it in a Python script, you can generally do it with the C API (most of the Python interface to Modeller is simply calling the C API underneath, in the _modeller module). So you can write the equivalent Python code, and then look at Modeller's Python interface to see what the equivalent C API functions are that it's calling. For example, to calculate the energy you would call the energy() method in the selection class; if you look at modlib/modeller/selection.py you'll see that that method calls the C API mod_energy() function. In C you will have to manually keep track of memory and handle errors, of course, which is done automatically for you by the Python interface.
Ben Webb, Modeller Caretaker
Hi.
Have you ever try to search for tutorial examples at modeller web site?
Good Lucky
--- On Thu, 4/5/12, NUTAN CHAUHAN nutanbt@yahoo.co.in wrote:
From: NUTAN CHAUHAN nutanbt@yahoo.co.in Subject: [modeller_usage] problem in modeling protein with ligand To: "modeller_usage@salilab.org" modeller_usage@salilab.org Date: Thursday, April 5, 2012, 10:01 AM
Hello all,I want to model my protein using template with its ligand bound to it. How can do this..i dnt hv idea. plz help.thnx in advance, Nutan Chauhan Research ScholarDepartment of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand From: "modeller_usage-request@salilab.org" modeller_usage-request@salilab.org To: modeller_usage@salilab.org Sent: Saturday, 24 March 2012 10:27 PM Subject: modeller_usage Digest, Vol 11, Issue 34
Send modeller_usage mailing list submissions to modeller_usage@salilab.org
To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request@salilab.org
You can reach the person managing the list at modeller_usage-owner@salilab.org
When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..."
Today's Topics:
1. Re: Is it possible to calculate energy for the given structure with MODELLER's C API and derivative with respect to all coordinates (x, y, z)? (Modeller Caretaker) 2. Re: homology modelling with multiple subunits (Modeller Caretaker) 3. Regarding protein 3D structure modeling (vishal Nemaysh) 4. Re: Regarding protein 3D structure modeling (Modeller Caretaker)
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Message: 1 Date: Thu, 22 Mar 2012 13:44:59 -0700 From: Modeller Caretaker modeller-care@salilab.org To: Valerio Lupperger valerio.lupperger@gmx.net Cc: modeller_usage@salilab.org Subject: Re: [modeller_usage] Is it possible to calculate energy for the given structure with MODELLER's C API and derivative with respect to all coordinates (x, y, z)? Message-ID: 4F6B8F4B.6020705@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 3/22/12 8:08 AM, Valerio Lupperger wrote: > I use MODELLER (9.10) in a c-program like in > http://salilab.org/modeller/manual/node456.html. As input I have one > structure and its restraints. Is it possible to calculate energy for the > given structure with MODELLER's C API and derivative with respect to all > coordinates (x,y,z)? And if so, how is it possible?
If you can do it in a Python script, you can generally do it with the C API (most of the Python interface to Modeller is simply calling the C API underneath, in the _modeller module). So you can write the equivalent Python code, and then look at Modeller's Python interface to
see what the equivalent C API functions are that it's calling. For example, to calculate the energy you would call the energy() method in the selection class; if you look at modlib/modeller/selection.py you'll see that that method calls the C API mod_energy() function. In C you will have to manually keep track of memory and handle errors, of course, which is done automatically for you by the Python interface.
Ben Webb, Modeller Caretaker
participants (2)
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NUTAN CHAUHAN