Re: [ccp4bb] Difference Map images

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

Previous message:
Subject: Re: Difference Map images
From: Doug Ohlendorf ohlen {- at -} UMN {- dot -} EDU
Date: 2009-06-17

Next message:
Subject: Re: Difference Map images
From: ANDY DODDS andy {- dot -} dodds6 {- at -} GOOGLEMAIL {- dot -} COM
Date: 2009-06-17

Subject: Re: Difference Map images
From: vincent Chaptal vchaptal {- at -} MEDNET {- dot -} UCLA {- dot -} EDU
Date: 2009-06-17

Andy,
on the practical point of view, you can create such images using Pymol
and the command 'carve'.

load composite_omit-ccp4.map, map-to-display, format=ccp4
isomesh mesh, map-to-display, 1.5, resi 45, carve=3
color blue, mesh

this will display the map at 1.5 sigma, at 3 angstroms around the
residue 45.
it gives you nice clean maps and it's a nice trick to remove the noise
in your density, with obvious ethic limitations... But if you carve 20A
around your residue, you're safe.

If i remember correctly, ligands create problems because of the HETAM in
the PDb file but you can replace it with ATOM and it should work.
the commands 'around' or 'expand' can achieve similar figures i believe.
Check he pymol wiki for more infos.
vincent

ANDY DODDS wrote:
> Hello,
>
> I was wondering what people used to generate difference map images of,
> say, a ligand in their structures?
>
> e.g. Figure 2a here
>
> http://journals.iucr.org/f/issues/2009/05/00/tt5012/tt5012.pdf
>
>
>
>
>
> Cheers,
>
> Andy
>
>

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CCP4bb navigation

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

Previous message:
Subject: Re: Difference Map images
From: Doug Ohlendorf ohlen {- at -} UMN {- dot -} EDU
Date: 2009-06-17

Next message:
Subject: Re: Difference Map images
From: ANDY DODDS andy {- dot -} dodds6 {- at -} GOOGLEMAIL {- dot -} COM
Date: 2009-06-17