Re: [ccp4bb] Electron density function for ligands in real space?

- 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: Pseudo-merohedral twinning and Molecular replacement
From: Iain Kerr ikerr {- at -} CMP {- dot -} UCSF {- dot -} EDU
Date: 2007-10-29

Next message:
Subject: Re: Pseudo-merohedral twinning and Molecular replacement
From: Peter Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2007-10-29

Subject: Re: Electron density function for ligands in real space?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-10-29

If you put the coordinates into COOT it will give you a validation score.
If you use the CCP$i map correlation procedures it will also give you a
CC for the density match.

The input in each case is the reflection file with appropriate amplitude
and phase terms.

What you use depends on what phases are available.
Experimental phases - use FP PHI and FOM
Output of REFMAC refinement - maybe FWT and PHWT after you have excluded
the ligand from the refinement calculation?

Eleanor
Ask if you need more detailed ideas..

Qing Zhang wrote:
> Hello,
>
> I'm new in x-ray crystallography and trying to compute real-space
> electron density for ligands. The goal is to evaluate match of ligands
> with density peaks (like computing local R values in real space). What
> would be the best electron density function that considers ligand
> atomic numbers/radii, density map resolution, and some local protein
> information (to estimate B values of ligand atoms)?
>
> Thank you in advance.
>
> Qing Zhang
>
>

CCP4bb navigation

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

Previous message:
Subject: Re: Pseudo-merohedral twinning and Molecular replacement
From: Iain Kerr ikerr {- at -} CMP {- dot -} UCSF {- dot -} EDU
Date: 2007-10-29

Next message:
Subject: Re: Pseudo-merohedral twinning and Molecular replacement
From: Peter Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2007-10-29