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[modeller_usage] how satisfactory relative orientation of modeled domains can be achieved in two matches cases



Hello,
I am exploring ModBase to build a model for the REcQ2 of arabidopsis Thaliana(swiss prot acc: Q9FT73). ModBase found 2 structures matching this target and after downloading the coordinates file and also the showfile.chimerax file, I was able to visualize with chimera both structures with apparently a satisfactory relative orientation. Below I copy-paste the target coverage:

		2v1xA 	(63-592) 	crystal structure of human recq-like dna helicase
		1wudA 	(531-602) 	e. coli recq hrdc domain


I wanted to know if there is an optimization step in the ModBase pipeline to achieve this and if it is referenced somewhere....and if not, which modules-scripts are available?

Thanks for your attention,
Maria Persico


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Today's Topics:

   1. Re: restraining secondary structure (Modeller Caretaker)
   2. Re: BLK usage => mainy chains (Modeller Caretaker)
   3. Re: Loop Modeling (Modeller Caretaker)
   4. Loop modeling while restraining the secondary	structure
      (bharat lal)


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

Message: 1
Date: Mon, 24 Jan 2011 14:49:01 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] restraining secondary structure
To: bharat lal <>
Cc: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 1/24/11 1:00 AM, bharat lal wrote:
I am using the following script for restraining the beta strands in my
protein (after searching the mailing archives):-

Your script will not work because you are using the automodel class
rather than your custom 'mymodel' class. Replace
a = automodel(env,
with
a = mymodel(env,

This also looks like a very old Modeller script (perhaps for Modeller
8). The way secondary structure restraints are defined has changed. See
http://salilab.org/modeller/9v8/manual/node27.html
for the correct syntax for adding a secondary structure restraint.

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


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

Message: 2
Date: Mon, 24 Jan 2011 14:51:01 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] BLK usage => mainy chains
To: Isaure Chauvot de Beauchene <>
Cc: 
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 1/24/11 6:56 AM, Isaure Chauvot de Beauchene wrote:
I try to build a modele with 2 protein templates. I want to modelise
just one loop of 1pkg, part of it on the template 3A2M, the rest of the
loop de novo. The rest of 1pkg must not be changed, so I put it as BLK:

BLK residues are really designed for modeling ligands and other things
that are not proteins. If you only want Modeller to optimize part of
your protein, see
http://salilab.org/modeller/9v8/manual/node23.html

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


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

Message: 3
Date: Mon, 24 Jan 2011 14:56:19 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Loop Modeling
To: bharat lal <>
Cc: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 1/24/11 12:01 AM, bharat lal wrote:
I want to graft the loop from some other protein taken from pdb to my
protein structure.

You could use multiple-template modeling to achieve this. Alternatively,
you could manually combine the two PDB files, using a PDB viewer or even
by editing the files in a text editor.

I tried modeling it on my own but some parts of the
secondary structure (beta sheet) also change into loop while loop
modeling ..

That is hardly surprising - loop modeling does not use any information
from the template.

So I want to fix those two ends of the beta sheet where the
loop is present so that these end should not change to loop region.

If you don't want to subject the beta sheet to loop modeling, simply
don't select those residues in the select_loop_atoms function:
http://salilab.org/modeller/9v8/manual/node34.html

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


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

Message: 4
Date: Tue, 25 Jan 2011 11:18:50 +0530 (IST)
From: bharat lal <>
Subject: [modeller_usage] Loop modeling while restraining the
	secondary	structure
To: modeller <>
Message-ID: <>
Content-Type: text/plain; charset="iso-8859-1"

Hi,
Thanks for the help regrading model-loop-define.py script. I have one doubt in model selection .. The number of residues that has to be mentioned for restraining should according to the target sequence only know ?? .. Also, I generated some 5 models while restraining some portion of the sequence as beta strands ?and after seeing all the structures I found that its model 3 that is having perfectly restrained beta sheets as compared to others but its DOPE score is ?more as compared to other structures . In this type of situation how do we have to select the correct model ?? Here's the list of energies that I got :
Summary of successfully produced models:Filename ? ? ? ? ? ? ? ? ? ? ? ? ?molpdf ? ? DOPE score ? ?GA341 score----------------------------------------------------------------------target.B99990001.pdb ? ? ? ? ?1552.05176 ? -25341.12891 ? ? ? ?1.00000target.B99990002.pdb ? ? ? ? ?1485.22974 ? -25387.23438 ? ? ? ?1.00000target.B99990003.pdb ? ? ? ? ?1559.28723 ? -25382.83984 ? ? ? ?1.00000 (perfectly restrained str.)target.B99990004.pdb ? ? ? ? ?1483.82568 ? -25213.86523 ? ? ? ?1.00000target.B99990005.pdb ? ? ? ? ?1402.83508 ? -25525.49023 ? ? ? ?1.00000

Also, I would like to ask one more thing about restraining structure that while giving the residue range generally last 2 or some times 1 residue/s doesnot retain the restrained structure .. In that case what do i need to do ?? After doing the restrained modeling is it required to do loop refinement .. as I am doing loop refinement also by generating some 50 structures and then finally selecting the one with low DOPE score .. Is this strategy right or wrong ???


--------------
Bharat



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End of modeller_usage Digest, Vol 10, Issue 15
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Maria Persico, PhD
Applied Bioinformatics Group, Biotec, TU Dresden,
Tatzberg 47-51, 01307 Dresden


Phone:   +49 (0)351 463 40020
Fax:     +49 (0)351 463 40087