Re: [ccp4bb] having difficulties with ammonium ion

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

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Subject: Advice on Enzyme Kinetics (substrate bound plate format)
From: Stephen Connelly connelly {- at -} SCRIPPS {- dot -} EDU
Date: 2012-08-11

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From: Faisal Tarique faisaltarique {- at -} GMAIL {- dot -} COM
Date: 2012-08-11

Subject: Re: having difficulties with ammonium ion
From: Eleanor Dodson eleanor {- dot -} dodson {- at -} YORK {- dot -} AC {- dot -} UK
Date: 2012-08-11

These are the atom names you should have in your monomer. No mention of H_N4 there..

NH4 HN4 H H 0.000 0.000 0.000 0.000
NH4 N N NT 1.000 -0.581 0.302 -0.782
NH4 HN3 H H 0.000 -1.232 1.041 -0.516
NH4 HN2 H H 0.000 -0.024 0.609 -1.579
NH4 HN1 H H 0.000 -1.055 -0.583 -0.962
loop_

On 10 Aug 2012, at 16:17, Afshan Begum wrote:

> Hello all,
> I am refining my structures with REFMAC 5 and is failed. Actually i used ammonium dihydrogen phosphate buffer during crystallization and in the map file where i observed the density of ammonium ion (NH4). I get this ion from the coot library but when i run refmac its failed even i gave the cif file for this ion as a supplement but i could not get success so, if any body give me suggestion how to solve this problem.
>
> I would be thankful to all.
> this are the error message came from refmac log file
>
>
> ERROR : atom :H4_N NH4 1 FF is absent in the library
> ATTENTION: atom:N NH4 1 FF is missing in the structure
> ERROR : atom :H4_N NH4 2 Fa is absent in the library
> ATTENTION: atom:N NH4 2 Fa is missing in the structure
> ERROR : atom :H4_N NH4 3 Fb is absent in the library
> ATTENTION: atom:N NH4 3 Fb is missing in the structure
> ERROR : atom :H4_N NH4 4 Fc is absent in the library
> ATTENTION: atom:N NH4 4 Fc is missing in the structure
> ERROR : atom :H4_N NH4 5 Fd is absent in the library
> ATTENTION: atom:N NH4 5 Fd is missing in the structure
> ERROR : atom :H4_N NH4 6 Fe is absent in the library
> ATTENTION: atom:N NH4 6 Fe is missing in the structure
> ERROR : atom :H4_N NH4 7 Ff is absent in the library
> ATTENTION: atom:N NH4 7 Ff is missing in the structure
>
> Best Regards
>
> AFSHAN
>
>

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

Previous message:
Subject: Advice on Enzyme Kinetics (substrate bound plate format)
From: Stephen Connelly connelly {- at -} SCRIPPS {- dot -} EDU
Date: 2012-08-11

Next message:
Subject: hi
From: Faisal Tarique faisaltarique {- at -} GMAIL {- dot -} COM
Date: 2012-08-11