[ccp4bb] negative density in difference map

- 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: adxv-SOLVED WITH FONTS
From: Rajesh kumar ccp4_sc {- at -} HOTMAIL {- dot -} COM
Date: 2011-11-23

Next message:
Subject: Re: negative density in difference map [SEC=UNCLASSIFIED]
From: "DUFF, Anthony" adu {- at -} ANSTO {- dot -} GOV {- dot -} AU
Date: 2011-11-23

Subject: negative density in difference map
From: Careina Edgooms careinaedgooms {- at -} YAHOO {- dot -} COM
Date: 2011-11-23

Good morning CCP4 members

I have a question about a 2F0-Fc difference map that I calculated with Refmac. In some instances it gives me negative (red) density around part of a side chain and no positive density in sight. Furthermore the entire residue fits well into the blue density of the complete map, including the part with negative density.

I am struggling to interpret this. Does the fact that it fits the blue density mean that the side chain is in the correct place or does the red blob on part of the side chain (eg on the sulphur in a Met residue) mean that something funky is happening with this side chain?

Thanks for any assistance
Careina

CCP4bb navigation

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

Previous message:
Subject: Re: adxv-SOLVED WITH FONTS
From: Rajesh kumar ccp4_sc {- at -} HOTMAIL {- dot -} COM
Date: 2011-11-23

Next message:
Subject: Re: negative density in difference map [SEC=UNCLASSIFIED]
From: "DUFF, Anthony" adu {- at -} ANSTO {- dot -} GOV {- dot -} AU
Date: 2011-11-23