Re: [ccp4bb] Fitting molecule B7G or B8G using COOT

- 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: Save image in Postscript format from PYMOL
From: shi jiahai jiahai {- dot -} shi {- at -} GMAIL {- dot -} COM
Date: 2007-06-21

Next message:
Subject: Ligand fitting in COOT and SHELX refinement
From: U Sam us_x {- at -} HOTMAIL {- dot -} COM
Date: 2007-06-22

Subject: Re: Fitting molecule B7G or B8G using COOT
From: Paul Emsley emsley {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-22

> I am trying to short out to fit a molecule into a density but having problem.
> It is n-beta-octyl-glucopyranoside into a electron density of my structure. The coordinate of this molecule I got from different from PDB. n-beta-octyl-glucopyranoside was present in the crystallization condition. I named it as "B8G" in the PDB.
> In COOT under "file:monomer search library" I find "beta-heptyl-glucopyranoside" and named as "B7G". But when I tried to fit B8G in COOT and use "real space refine zone", its not working out but I get the following warning message.
> "INFO:: using standard CCP4 Refmac dictionary to search for B8G
> WARNING:: Failed to find restraints for :B8G: "

Refmac has BOG: beta octylglucoside
Will that do?

Paul.

CCP4bb navigation

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

Previous message:
Subject: Save image in Postscript format from PYMOL
From: shi jiahai jiahai {- dot -} shi {- at -} GMAIL {- dot -} COM
Date: 2007-06-21

Next message:
Subject: Ligand fitting in COOT and SHELX refinement
From: U Sam us_x {- at -} HOTMAIL {- dot -} COM
Date: 2007-06-22