Re: [ccp4bb] tutorial / pipeline for ligand fitting, refinement?

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

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- X-ray detectors

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

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Subject: tutorial / pipeline for ligand fitting, refinement?
From: ANDY DODDS andy {- dot -} dodds6 {- at -} GOOGLEMAIL {- dot -} COM
Date: 2009-02-05

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Subject: Choosing MR solutions in the case of perfect twinning with P41212?
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2009-02-05

Subject: Re: tutorial / pipeline for ligand fitting, refinement?
From: Scott Pegan pegan {- at -} UIC {- dot -} EDU
Date: 2009-02-05

Andy,

We do a lot of liganding fitting with CCP4. This is the general order of
steps we take (post initial solution of the protein itself):

1) Build the potential ligand in CCP4 Sketcher

a) Rename all the Hydrogens to H#, CCP4 Refmac has some issues with
Hydrogens marked OH1, NH1, etc. To simplify things I normally just renumber
all the Hydrogens starting from 1. Also makes for less hassle when using
the definition file, as the labels in the definition file has to match the
pdb of the ligand (this will be more important below).

b) Use the regularize function with Refmac

2) Using Coot, load the protein and maps

3) Load the ligand and definition file (####_mon_lib.cif)

4) Use the find ligand function in Coot (find it under other modeling tools)

a) select the protein, map you want to search

5) If you find results you desire, merge those ligands with the main pdb

6) Run Refmac on the merged PDB with the library for the ligand in the
library input space.

Hope this helps,

Scott

On Thu, Feb 5, 2009 at 9:27 AM, ANDY DODDS wrote:

> Hello,
>
> does anyone know of a tutorial which lays out some sort of pipeline,
> hopefully using CCP4 packages, to fit and refine a small molecule
> ligand please?
>
> cheers
>
> andy
>
>

--
Scott D. Pegan, Ph.D.
Senior Research Specialist
Center for Pharmaceutical
Biotechnology
University of Illinois at Chicago

CCP4bb navigation

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

Previous message:
Subject: tutorial / pipeline for ligand fitting, refinement?
From: ANDY DODDS andy {- dot -} dodds6 {- at -} GOOGLEMAIL {- dot -} COM
Date: 2009-02-05

Next message:
Subject: Choosing MR solutions in the case of perfect twinning with P41212?
From: Francis E Reyes Francis {- dot -} Reyes {- at -} COLORADO {- dot -} EDU
Date: 2009-02-05