Re: [ccp4bb] How to determine water number?

- 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: How to determine water number?
From: AntonioLeung leunglm {- at -} LIVE {- dot -} CN
Date: 2009-08-17

Next message:
Subject: Re: imosflm with multiple data sets
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-08-18

Subject: Re: How to determine water number?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-08-17

Hi Antonio,

> My question is how can I determine which water is needed, which is not
> needed?

may be this will give you some clues - here are the approximate criteria
for water picking that are used in automatic water picking and
refinement in phenix.refine:

1) peak at mFo-DFc map is higher than ~3sigma, and
2) peak center is within a hydrogen bond to another atom (water or
macromolecule), and
3) peak has approximately the same shape as a water molecule would have
at this resolution and local environment, and
4) peak at 2mFo-DFc is higher than ~1.5 sigma,

after a round of coordinate and B-factor refinement,

the criteria (2-3-4) are still ok, and

5) refined B-factor of newly placed water is meaningful (didn't jump to
large value), otherwise a water is deleted.

There are a few other technical tricks to make this process robust and
efficient at high resolution, higher than ~1.2A or so, but this is, I
guess, beyond of what you were asking about.

Pavel.

CCP4bb navigation

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

Previous message:
Subject: How to determine water number?
From: AntonioLeung leunglm {- at -} LIVE {- dot -} CN
Date: 2009-08-17

Next message:
Subject: Re: imosflm with multiple data sets
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-08-18