[RNABuilder-help] Re: About the cross the strand of RNA

[Samuel Flores]

Hi Sung-Huan

I'm cc'ing the help list since there's nothing particularly private here -- let me know if you prefer not to.

"Physics where you want it" is now much faster.  I much prefer to use than now, rather than the "contact" commands.  The command you want is probably "includeAllNonBondAtomsInResidues."  You'll find it in the reference guide.

You can also send me your command file if you want me to take a quick look.

What university do you work at, out of curiosity?

Sam




On Oct 4, 2013, at 5:37 PM, Sung-Huan Yu <noreply at simtk.org> wrote:

> You have been contacted by a member of Simtk.org.
> 
> From: Sung-Huan Yu
> Email: sunghuanyu at gmail.com
> 
> The e-mail was sent via the "contact" link on Simtk.org by the above member. It is not screened by Simtk.org or its staff.
> 
> 
> *** MESSAGE BEGINS ***
> 
> Hi,
> 
> Recently, I try to simulate RNA 3d structure from sequence. However, I usually get the results of strand crossing. I mean the one strand pierce through another strand ( it is very clear to see in New cartoon presentation). Therefore, they will aggregate together. Could you give me some suggestions to set some parameters to avoid this situation? I already try some parameters about atom steric. it will make the basepairings become wrong. I also tried some numbers of the baseInteractionScaleFactor. it still not works. Thank you