Re: [ccp4bb] GLRF and interpreting self rotation functions...

- 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: friction
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-04-02

Next message:
Subject: Re: friction or releasing pdb's
From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
Date: 2009-04-02

Subject: Re: GLRF and interpreting self rotation functions...
From: Jeff Speir speir {- at -} SCRIPPS {- dot -} EDU
Date: 2009-04-02

A standard orientation is anything you want it to be and is usually
defined in the context of orthogonal axes. It is simply a reference
point from which you apply the results of your search. We usually
use one or more of the orthogonal axes as a starting point for easier
visualization.

To define a 3-fold axis for a locked search in GLRF (if I understood
your message correctly):

locsym 90.0 90.0 120.0 3 polar

This defines a standard orientation for that 3-fold. The search will
then move the 3-fold by the given parameters to new orientations and
calculate the peak height at those grid points after applying 3-fold
NCS. Which axis this actually defines as your standard orientation
and how it is then moved during the search depends on your choice of
conventions for orthogonalization and polar angle searches.

Cheers,

Jeff

On Apr 1, 2009, at 3:32 PM, Francis E Reyes wrote:

> I am experimenting with GLRF and am having trouble calculating the
> locked self rotation function for a protein of known structure.
> The protein has a 3 fold NCS axis that is not parallel to a
> crystallographic axis. I'm at the step of specifying the local
> symmetry elements for the locked self rotation function.
>
> I guess the goal here is to search for 'one general rotation which
> will bring the non crystallographic symmetry point group in a
> "standard" orientation. What does this mean? How do I write the
> LOCSymmetry instruction for the input file?
>
> My s.g. is P 21 21 21 and the following solutions are found for the
> normal self rotation function.
>
>
>
> Fine searches around peaks with the slow rotation function --
>
> The large-term cut-off is 1.50
>
> Listing of the fitted angles of the top 5 peaks --
>
> No. Old Angles S A N G L
> E O A N G L E Old Ht. New Ht.
> (polar,
> XYK) (polar, XZK)
> phi psi
> kap phi psi kap
>
> 1 52.000 50.000 120.000 52.000 50.500
> 120.000 53.246 127.449 120.000 417.36 420.74
> 2 128.000 130.000 120.000 128.000 129.500
> 120.000 233.246 127.449 120.000 417.36 420.74
> 3 128.000 50.000 120.000 129.000 50.000
> 120.000 126.870 126.536 120.000 400.32 407.69
> 4 52.000 130.000 120.000 51.000 130.000
> 120.000 306.870 126.536 120.000 400.32 407.68
> 5 44.000 60.000 120.000 42.000 61.000
> 120.000 36.719 125.820 120.000 385.56 391.96
>
> The goal of all this is to use GLRF to explore NCS in cases where
> structures are not known and molecular replacement
>
> Thanks
>
> FR
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
>

CCP4bb navigation

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

Previous message:
Subject: Re: friction
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-04-02

Next message:
Subject: Re: friction or releasing pdb's
From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
Date: 2009-04-02