VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Mon May 27 2002 - 12:25:44 CDT

Hi,

I assume this error came from using the RMS menu, and not from any command
line script that you wrote yourself? The RMS menu was contributed by member
of our research group, so I'll refer you to him if you have specific questions
about it: sure_at_ks.uiuc.edu.

Justin

On Mon, May 27, 2002 at 05:45:13PM +0200, Vlad Cojocaru wrote:
> I did that but if I select all the residues and I say backbone only the
> following error appears:
>
> bgerror failed to handle background error.
> Original error: can't read "pdb_list": no such variable
> Error in bgerror: invoked "break" outside of a loop
> bgerror failed to handle background error.
> Original error: can't read "pdb_list": no such variable
> Error in bgerror: invoked "break" outside of a loop
>
> Do you have any ideea what is this?
>
>
>
>
>
> Justin Gullingsrud wrote:
>
> >Hi,
> >
> >In the VMD user's guide there's a section devoted to RMS fits in VMD:
> >http://www.ks.uiuc.edu/Research/vmd/current/ug/node183.html
> >
> >Have a look there and let us know if you still have questions.
> >
> >Cheers,
> >
> >Justin
> >
> >On Mon, May 27, 2002 at 04:30:59PM +0200, Vlad Cojocaru wrote:
> >
> >>Dear VMD users,
> >> I have two RNA molecules. I would like to fit them using the
> >>backbone and calculate the rmsd. Can anyone give a hint how can you do
> >>that with vmd. I would also like to visualize the 2 fitted structures at
> >>once in order to see how they overlay.
> >> Thank you very much for any kind of help
> >>vlad
> >>
> >>--
> >>Vlad Cojocaru
> >>Max Planck Institut for Biophysical Chemistry
> >>Deparment: 060
> >>Am Fassberg 11, 37077 Goettingen, Germany
> >>tel: ++49-551-201.1389
> >>e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> >>
> >>
> >
>
> --
> Vlad Cojocaru
> Max Planck Institut for Biophysical Chemistry
> Deparment: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1389
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
>
>
> 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D