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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)
Message: 1 Date: Thu, 22 Mar 2012 13:44:59 -0700 From: Modeller Caretaker <" href="mailto:">> To: Valerio Lupperger <" href="mailto:">> Cc: " href="mailto:"> 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: <" href="mailto:">> 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.
On 3/22/12 10:53 AM, Zumot, Elia Nabil wrote: > Is there a way to generate a homology model using several subunits as > template? The protein I wish to model is a homotrimer. Am I wrong or > is what is explained in "Building a model from multiple templates" > not relevant here since I need the three subunits together in space > (without steric clashes).
Modeller is not going to magically determine the interface region between your subunits and dock them, of course. You need to give it information about the interface between subunits (either by giving it a multimeric template, or by supplying it with subunit-subunit restraints if you only have monomeric
templates).
Message: 3 Date: Sat, 24 Mar 2012 11:27:49 +0530 From: vishal Nemaysh <" href="mailto:">> To: " href="mailto:"> Subject: [modeller_usage] Regarding protein 3D structure
modeling Message-ID: <CALCM-RALrVh0c_NhOOVBKU_XvMQiFnnkyi-=18+" href="mailto:">> Content-Type: text/plain; charset="iso-8859-1"
Hello Sir or all group members,
i have an amino acid sequence and the length is (1106 amino acid). so plz tell me how can i model the complete 3D structure of this much lengthy sequence.
Message: 4 Date: Sat, 24 Mar 2012 09:57:30 -0700 From: Modeller Caretaker <" href="mailto:">> To: vishal Nemaysh <" href="mailto:">> Cc: " href="mailto:"> Subject: Re: [modeller_usage] Regarding protein 3D structure modeling Message-ID: <" href="mailto:">> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 3/23/12 10:57 PM, vishal
Nemaysh wrote: > i have an amino acid sequence and the length is (1106 amino acid). so > plz tell me how can i model the complete 3D structure of this much > lengthy sequence.
Modeller has no maximum length; modeling a large protein is exactly the same as modeling a small protein. You might have to tweak automodel.max_ca_ca_distance if the protein is especially large though: http://salilab.org/archives/modeller_usage/2011/msg00268.html