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
[EMAIL PROTECTED]
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: [EMAIL PROTECTED]
> To: [EMAIL PROTECTED]
> 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 <[EMAIL PROTECTED]> 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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