Re: [ccp4bb] sugar ligand refinement in coot

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

Previous message:
Subject: Re: hydrophobic surface representation
From: Madhumati Sevvana msevvana {- at -} BIOLOGIE {- dot -} UNI-ERLANGEN {- dot -} DE
Date: 2008-11-06

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From: jane {- dot -} wibley {- at -} SYNGENTA {- dot -} COM jane {- dot -} wibley {- at -} SYNGENTA {- dot -} COM
Date: 2008-11-06

Subject: Re: sugar ligand refinement in coot
From: junfeng liu jliu {- at -} NIMR {- dot -} MRC {- dot -} AC {- dot -} UK
Date: 2008-11-06

Hi Lei,
You can make a new library using Libcheck in CCP4 or eLBOW in Phenix .
Then you can handle your ligands in Coot.
Of course , the new PDB file for the GLC-GLC can be obtained from PDB
or you can make it by libcheck yourself.
Good luck!
liu
Petr Kolenko wrote:
> 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: hydrophobic surface representation
From: Madhumati Sevvana msevvana {- at -} BIOLOGIE {- dot -} UNI-ERLANGEN {- dot -} DE
Date: 2008-11-06