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I'm not sure what name phenix or ccp4 like, but looking in 
$CNS_TOPPAR/dna-rna.top, I see this line:

   ATOM C5A   TYPE=CC3E  CHARGE=0.00    END

so CNS likes C5A.  If you want CNS to play well with other programs, 
just change that line in your topology file to

   ATOM C7    TYPE=CC3E  CHARGE=0.00    END

or whatever you want.

kmj

On 11/1/08 8:13 PM, Raja Dey wrote:
> Dear Friends,
>          I am tired of renaming an atom name every time I want to switch 
> among the programs cns, phenix and ccp4 particularly for a carbon atom 
> C5A of Thymine given below. What name I should give to this atom 
> specially for cns? Is it C7 or C5A or C5M?
> 
> ATOM   1541  P   THY K   5     -33.604  -2.379  -7.017  1.00293.90     
>  K    P
> ATOM   1542  O1P THY K   5     -33.190  -3.005  -5.747  1.00305.95     
>  K    O
> ATOM   1543  O2P THY K   5     -33.393  -3.107  -8.289  1.00298.26     
>  K    O
> ATOM   1544  O5' THY K   5     -32.867  -0.964  -7.135  1.00278.14     
>  K    O
> ATOM   1545  N1  THY K   5     -32.261   0.951  -3.645  1.00297.58     
>  K    N
> ATOM   1546  C6  THY K   5     -32.334  -0.383  -3.282  1.00295.41     
>  K    C
> ATOM   1547  C2  THY K   5     -33.001   1.906  -2.968  1.00292.90     
>  K    C
> ATOM   1548  O2  THY K   5     -32.983   3.098  -3.232  1.00291.97     
>  K    O
> ATOM   1549  N3  THY K   5     -33.786   1.406  -1.958  1.00289.04     
>  K    N
> ATOM   1550  C4  THY K   5     -33.903   0.087  -1.558  1.00286.25     
>  K    C
> ATOM   1551  O4  THY K   5     -34.635  -0.264  -0.640  1.00287.39     
>  K    O
> ATOM   1552  C5  THY K   5     -33.104  -0.855  -2.294  1.00284.89     
>  K    C
> ATOM   1553  C5A THY K   5     -33.151  -2.313  -1.950  1.00269.91     
>  K    C
> ATOM   1554  C2' THY K   5     -30.072   0.525  -4.886  1.00288.00     
>  K    C
> ATOM   1555  C5' THY K   5     -31.443  -0.886  -7.113  1.00269.59     
>  K    C
> ATOM   1556  C4' THY K   5     -31.054   0.568  -6.965  1.00273.61     
>  K    C
> ATOM   1557  O4' THY K   5     -31.989   1.179  -6.040  1.00282.58     
>  K    O
> ATOM   1558  C1' THY K   5     -31.349   1.354  -4.783  1.00292.39     
>  K    C
> ATOM   1559  C3' THY K   5     -29.708   0.843  -6.325  1.00277.20     
>  K    C
> ATOM   1560  O3' THY K   5     -29.453   2.227  -6.477  1.00283.69     
>  K    O
> 
> Is there any common name of this atom which can be used for all the 
> programs?
> Thanks for any suggestion.
> 
>  
> Raja 
> 
> 
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