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Re: [ccp4bb]: nucleic acids and alternate conformations within a strand: refmac5
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Thanks very much for all the advice.
I've solved the problem.
What I found was that if I put in two sets of coordinates corresponding
to the two conformers en bloc, (similar to the example below)
refmac only allowed me to put in one dual-conformation residue at a
time. However if I instead put them
pairwise for each atom, then it works. (I found it less tedious to add
one residue at a time and let refmac reorder the lines for me.)
Thanks again for everyone's help.
On Tuesday, July 2, 2002, at 02:12 PM, Garib N Murshudov wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> 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
>
>