Re: [ccp4bb] Refmac and links between ligands

- 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: how to supply the following twin operator to detwin?
From: Pete pete {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2010-02-01

Next message:
Subject: Cryoprotector
From: Marta_Martínez mmartine {- at -} UNIZAR {- dot -} ES
Date: 2010-02-02

Subject: Re: Refmac and links between ligands
From: Jan Dohnalek dohnalek007 {- at -} GMAIL {- dot -} COM
Date: 2010-02-02

Problem solved.
One must also switch to the "make sugar NO" keyword. Otherwise Refmac tries
to use the discovered sugar and ion as if it was sugar-peptide bond.

Jan Dohnalek

On Mon, Feb 1, 2010 at 2:52 PM, Jan Dohnalek wrote:

> Dear all
> I understand that when I use the Refmac keyword
> make link no
> Refmac should not apply found links.
> It keeps finding links between ligands (Na+ and ligand OH) and (I think)
> refines them as it issues a warning (not INFO), does not say "(not be used)"
> for these and the output .pdb file contains the LINK records newly created
> for these atoms.
>
> The actual distances look pretty much as if they were restrained ...
>
> Is there a way to make Refmac ignore these links?
>
> Jan Dohnalek
>
> --
> Jan Dohnalek, Ph.D
> Institute of Macromolecular Chemistry
> Academy of Sciences of the Czech Republic
> Heyrovskeho nam. 2
> 16206 Praha 6
> Czech Republic
>
> Tel: +420 296 809 390
> Fax: +420 296 809 410
>

--
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 390
Fax: +420 296 809 410

CCP4bb navigation

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

Previous message:
Subject: Re: how to supply the following twin operator to detwin?
From: Pete pete {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2010-02-01

Next message:
Subject: Cryoprotector
From: Marta_Martínez mmartine {- at -} UNIZAR {- dot -} ES
Date: 2010-02-02