[RNABuilder-help] Fwd: Queries regarding using RNABuilder for threading RNA-ligand complex

[Samuel Coulbourn Flores]

Begin forwarded message:

> From: Samuel Flores <samuelfloresc at gmail.com>
> Date: November 22, 2010 4:28:19 AM CST
> To: Wee Kiang Yeo <weekiang at gmail.com>
> Subject: Re: Queries regarding using RNABuilder for threading RNA-ligand complex
> 
> Absolutely!  
> 
> for example, let's say the template is strand "A".  Then:
> 
> constrainToGround A 15
> 
> fixes the position of the C3* atom of residue 15 of chain A to ground.  If you have rigidified the entire template, you can choose any residue within it .. but it's better to choose one near the geometric center.
> 
> You might also find it useful to set the constraintTolerance parameter to something lower.  By default, the above constraint is enforced within .005 in all its internal coordinates.  
> 
> Where are you studying?  I run RNABuilder workshops frequently, maybe you and your department would be interested in one at some point.
> 
> Sam
> 
> 
> 
> On Nov 22, 2010, at 3:20 AM, Wee Kiang Yeo wrote:
> 
>> Dear Dr Flores,
>> 
>> Two days ago, I have used RNABuilder to thread an RNA sequence through
>> a X-ray structure of 23S RNA (obtained from PDB). This X-ray structure
>> contains a ligand in a binding pocket. The original intention of
>> threading the RNA sequence was to ascertain the nucleotide residues
>> located near the ligand. However, during threading, the template X-ray
>> structure actually translocated in 3D space, leaving the
>> previously-bound ligand behind.
>> 
>> My question: Is there a way to fix the position of the RNA-ligand
>> complex template during the threading process? If so, I would
>> appreciate it if you can give me an example of how to do so.
>> 
>> Thanks.
>> 
>> Regards,
>> Wee Kiang YEO (Mr)
> 

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