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Re: [ccp4bb]: nucleic acids and alternate conformations within a strand: refmac5
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Hi
If you define your residues as (corresponding corrections for dna or rna of
course should be made) then it should work. I.e. you define alternatives for
first residue, then for the second residue etc then it works. In principle
there should not be difference between nucleatide or protein.
ATOM 752 N GLU A 104 0 18.756 12.225 0.940 1.00 15.86 N
ATOM 753 CA GLU A 104 0 17.389 11.946 0.501 1.00 15.48 C
ATOM 754 C GLU A 104 0 17.100 12.700 -0.791 1.00 16.38 C
ATOM 755 O GLU A 104 0 17.978 13.384 -1.354 1.00 15.23 O
ATOM 756 CB GLU A 104 0 16.485 12.310 1.683 1.00 15.10 C
ATOM 757 CG GLU A 104 0 16.780 11.524 2.961 1.00 17.08 C
ATOM 758 CD GLU A 104 0 17.887 12.087 3.839 1.00 19.16 C
ATOM 759 OE1 GLU A 104 0 18.146 11.459 4.918 1.00 23.11 O
ATOM 760 OE2 GLU A 104 0 18.513 13.136 3.555 1.00 18.75 O
ATOM 761 N ALEU A 105 0 15.873 12.555 -1.280 0.50 14.44 N
ATOM 762 CA ALEU A 105 0 15.406 13.115 -2.517 0.50 15.47 C
ATOM 763 C ALEU A 105 0 15.768 14.544 -2.859 0.50 15.35 C
ATOM 764 O ALEU A 105 0 15.963 14.770 -4.062 0.50 17.22 O
ATOM 765 CB ALEU A 105 0 13.842 13.034 -2.542 0.50 15.44 C
ATOM 766 CG ALEU A 105 0 13.284 11.785 -3.214 0.50 14.92 C
ATOM 767 CD1ALEU A 105 0 11.782 11.945 -3.514 0.50 15.66 C
ATOM 768 CD2ALEU A 105 0 14.072 11.434 -4.470 0.50 14.39 C
ATOM 769 N BLEU A 105 0 15.821 12.626 -1.167 0.50 14.96 N
ATOM 770 CA BLEU A 105 0 15.329 13.376 -2.325 0.50 15.94 C
ATOM 771 C BLEU A 105 0 15.621 14.845 -2.029 0.50 15.00 C
ATOM 772 O BLEU A 105 0 15.515 15.375 -0.907 0.50 12.33 O
ATOM 773 CB BLEU A 105 0 13.832 13.078 -2.478 0.50 17.67 C
ATOM 774 CG BLEU A 105 0 13.061 13.102 -3.782 0.50 18.74 C
ATOM 775 CD1BLEU A 105 0 13.549 12.096 -4.827 0.50 19.53 C
ATOM 776 CD2BLEU A 105 0 11.569 12.809 -3.496 0.50 18.49 C
ATOM 777 N AGLY A 106 0 15.855 15.448 -1.884 0.50 16.13 N
ATOM 778 CA AGLY A 106 0 16.117 16.867 -2.119 0.50 15.31 C
ATOM 779 C AGLY A 106 0 17.510 17.335 -1.714 0.50 17.06 C
ATOM 780 O AGLY A 106 0 17.943 18.485 -1.641 0.50 15.64 O
ATOM 781 N BGLY A 106 0 16.040 15.577 -3.068 0.50 15.29 N
ATOM 782 CA BGLY A 106 0 16.379 16.980 -2.902 0.50 15.26 C
ATOM 783 C BGLY A 106 0 17.737 17.215 -2.246 0.50 16.69 C
ATOM 784 O BGLY A 106 0 18.111 18.398 -2.293 0.50 15.89 O
On Tuesday 02 Jul 2002 9:44 pm, wgscott@chemistry.ucsc.edu wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> I apologize if this has been answered before but my search did not turn
> up anything.
>
> I am refining a nucleic acid, one strand of which has two consecutive
> nucleotides (backbone + ribose + base) that have two alternate
> conformers.
>
> I haven't been able to get refmac5 to allow me to do this.
>
> If I focus on the first of the two, and break the chain so that it
> becomes the 3' end of a chain, rather than an internal nucleotide, I can
> get refmac to refine the two conformations. However if I make two
> alternative 3' ends that are instead of one residue long, two residues
> long, refmac no longer allows me to do this. Therefore I think I can
> safely conclude it is a problem with wanting to have more than one
> residue as an alternate conformer, rather than some other sort of syntax
> error.
>
> The error refmac reports in the cases where it doesn't work is:
>
> ERROR: in chain SS residue: 120
> different residues have the same number
>
>
> There is an error in the input coordinate file
> At least one the chains has 2 residues with the same number
> Check above to see error
>
>
> Any suggestions for a workaround?
>
> Thanks in advance.
>
> Bill Scott
--
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 432565