Re: [ccp4bb] sugar ligand refinement in coot

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

Previous message:
Subject: Re: sugar ligand refinement in coot
From: lei feng spartanfenglei {- at -} HOTMAIL {- dot -} COM
Date: 2008-11-06

Next message:
Subject: hydrophobic surface representation
From: Sebastiano Pasqualato sebastiano {- dot -} pasqualato {- at -} IFOM-IEO-CAMPUS {- dot -} IT
Date: 2008-11-06

Subject: Re: sugar ligand refinement in coot
From: Petr Kolenko kolenko {- at -} IMC {- dot -} CAS {- dot -} CZ
Date: 2008-11-06

Hi Lei.
As I expect, you use REFMAC for structure refinement. This link should
help you to connect in principle any atoms between residues (or ligands
as well).

http://www.ccp4.ac.uk/html/refmac5/files/coordinates.html#pdb_link

You can also find many examples of different LINKs in the PDB records. I
would prefer the most similar ones. ;)

Best wishes,
Petr

Petr Kolenko
kolenko@imc.cas.cz
protein.awardspace.com

lei feng wrote:

> Hello Carlos
>
> thanks for your kindly reply. I think the cif file ( GLC_mon_lib.cif
> ) is only for one glucose molecule, it can not regulate the bond
> between two glucose units, that is why they break apart in the real
> space refinement.
>
> in the pdb file , different glucoses are different molecules, I do
> not know how to generate a cif file to give regulation on bond between
> glucose units. If we can make this cif file , is it the same as
> GLC_mon_lib.cif?
>
> Thanks a lot for you help .
>
> Yours
> Lei
>
>
> > Date: Wed, 5 Nov 2008 17:23:58 -0600
> > From: Carlos.Huerta@UTSouthwestern.edu
> > To: spartanfenglei@HOTMAIL.COM
> > Subject: Re: [ccp4bb] sugar ligand refinement in coot
> >
> > Lei,
> >
> > If your cif file isn't complete, you can load your pdb GLC in
> Sketcher in ccp4 suite and generate a cif file. When you have your
> cif, import your cif file inside coot.
> >
> > Carlos
> >
> > >>> lei feng 11/05/08 4:08 PM >>>
> >
> > hello everyone
> >
> > can anyone help me with sugar ( say maltoheptaose) refinement in coot?
> >
> > I use the pdb file with " GLC " name , it always breaks apart into
> discountinuous glucose when I try to use real space refinement , I
> believe that is because there is no restraint with regarding to bond ,
> whatever in cif file.
> >
> > I know I could give it a unique name , say G7 and substitute the "
> GLC "it in the pdb file, make a new cif file and refine it , it will
> not break apart again. But , when I deposit the structure in the
> future , it is allowed? It seems everyone working with sugar ligands
> are using " GLC" . how did they work in refinement ?
> >
> > Thanks for any suggestion.
> >
> > lei Feng
> > _________________________________________________________________
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CCP4bb navigation

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

Previous message:
Subject: Re: sugar ligand refinement in coot
From: lei feng spartanfenglei {- at -} HOTMAIL {- dot -} COM
Date: 2008-11-06

Next message:
Subject: hydrophobic surface representation
From: Sebastiano Pasqualato sebastiano {- dot -} pasqualato {- at -} IFOM-IEO-CAMPUS {- dot -} IT
Date: 2008-11-06