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Re: [ccp4bb] Refmac5, .cif file for ligans and restrain.
 

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CCP4bb <-- 2007 <-- September 2007 <-- 17 September 2007
Previous message:
Subject: Re: model-mask
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-17 		Next message:
Subject: Postdoc at University of Texas Medical Branch
From: "Stein, ND (Norman)" n {- dot -} d {- dot -} stein {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-09-17


Subject: Re: Refmac5, .cif file for ligans and restrain.
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-17
I am not clear whether you want to apply NCS restraints to multiple
copies of the same ligand type.
That is easy - you just restrain Ligand CHAIN and "residue number1
residue number 1" in the same way as for protein chains ( Presumably
residue number1 and residue number2 will be the same)

If you want more restraints within the ligand than SKETCHER you will
need to edit the dictionary file

To use 2 ligands you just put them both in the same cif file - see GUI
task under Refinement modele - Merge Monomer Libraries

Eleanor


U Sam wrote:
> I appreciate if anybody suggest following.
> I am trying to fit a ligand into a protein (covalently bonded) and refine using refmac5. I made .cif file (ligand.cif) using ccp4i which I provide to refmac5 during the refinement.
>
> Question is how can I restrain the geometrical paramers of the similar bonds, angles and/or torsions of the ligand(s) during this refinement?
>
> My second question is if anybody wants to fit more than one ligand (different types), then how can s/he mention two or more .cif files in the refmac5 refiments ? I see it has only one place for providing .cif file as Library.
>
> Thanks
> Sam
>
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CCP4bb navigation

CCP4bb <-- 2007 <-- September 2007 <-- 17 September 2007
Previous message:
Subject: Re: model-mask
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-17 		Next message:
Subject: Postdoc at University of Texas Medical Branch
From: "Stein, ND (Norman)" n {- dot -} d {- dot -} stein {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-09-17


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