Re: [ccp4bb] build fragment library from pdb based on a specific geometry

- 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: Reindexing Orthorhombic
From: Jon Wright wright {- at -} ESRF {- dot -} FR
Date: 2009-04-17

Next message:
Subject: Pointless not Painless
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2009-04-17

Subject: Re: build fragment library from pdb based on a specific geometry
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2009-04-17

The most general solution to this problem boils down to one of graph
isomorphism:

http://en.wikipedia.org/wiki/Graph_isomorphism

James

On Apr 16, 2009, at 8:13 PM, rui wrote:

> Dear all,
>
> I want to pull out the sugar binding proteins from the pdb, however,
> there are so many different names for the ligand ( GAL, GLC,
> RIP... ) and it's not easy to get a complete list. If I want to pull
> out some fragments based on a specific geometry ( for instance, the
> glucose has C1 C2 C3 C4 C5 C6, and I want to use the geometry for
> instance, O5,C1, O1, C2 and O2 to pull out all the ligands that
> contains this kind of geometry. Is there any straightforward way to
> do it?
>
> Thanks a lot.

CCP4bb navigation

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

Previous message:
Subject: Re: Reindexing Orthorhombic
From: Jon Wright wright {- at -} ESRF {- dot -} FR
Date: 2009-04-17

Next message:
Subject: Pointless not Painless
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2009-04-17