Begin forwarded message:

From: Samuel Flores <samuelfloresc@gmail.com> Date: November 22, 2010 4:28:19 AM CST To: Wee Kiang Yeo <weekiang@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)