Re: [ccp4bb] Program to evaluate RNA torsion angles?

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Program to evaluate RNA torsion angles?
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-05-08

Next message:
Subject: How can I refine Mg2+ with REFMAC?5.2
From: Dirk Kostrewa dirk {- dot -} kostrewa {- at -} PSI {- dot -} CH
Date: 2007-05-09

Subject: Re: Program to evaluate RNA torsion angles?
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-05-08

One option is to just use the tools available from the pdb (the nucleic
acid database).

http://ndbserver.rutgers.edu

Another is Anna Marie Pyle's program Amigos.

http://www.csb.yale.edu/people/pyle/software

There are a lot of combinations consistent with A and B form helices, so
this might be worth doing even if you use the first option.

Yuan Lin wrote:
> Dear All,
> I was wonder if anyone knows of a program for evaluating the quality of
> nucleic acid torsion angles in a manner comparable to a Ramachandran plot
> for proteins? I am working on an A-form dsRNA structure and there are some
> deviations from the average torsion angles for A-RNA, due to the
> incorporation of an A-bulge. This might be silly, but how could I know
> whether those deviations are outrageous or not?
>
> Thanks very much!
>
>
> Yuan
>
>
> ------------------------
> Yuan Lin
> Biochemistry and Molecular Biology
> Johns Hopkins University
> Rm. W8702 BSPH
> 615 N. Wolfe St.
> Baltimore, MD 21205
> Ph. 443-287-4988
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Program to evaluate RNA torsion angles?
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-05-08

Next message:
Subject: How can I refine Mg2+ with REFMAC?5.2
From: Dirk Kostrewa dirk {- dot -} kostrewa {- at -} PSI {- dot -} CH
Date: 2007-05-09