Re: [ccp4bb] sugar ligand refinement in coot

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

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Subject: Latest Compilation of Marketed Drugs
From: Sridhar Prasad SridharP {- at -} MBASIS {- dot -} COM
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Subject: Re: sugar ligand refinement in coot
From: Petr Kolenko kolenko {- at -} IMC {- dot -} CAS {- dot -} CZ
Date: 2008-11-06

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

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> _________________________________________________________________> Color coding for safety: Windows Live Hotmail alerts you to suspicious email.> http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_safety_112008
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CCP4bb navigation

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

Previous message:
Subject: Latest Compilation of Marketed Drugs
From: Sridhar Prasad SridharP {- at -} MBASIS {- dot -} COM
Date: 2008-11-05

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