Thanks to Robbie Joosten who suggested updating to refmac 5.5.0090
which seems to be happy with alternate conformation again.
I thought it was probably worth mentioning on the list that the ccp4
bundled refmac has this bug.
Simon
On 17 Apr 2009, at 14:07, Simon Kolstoe wrote:
> Dear ccp4bb,
>
> I've finally gotten around to updating my ccp4 to version 6.1.1 with
> the default refmac 5.5.0072 that comes with this from the ccp4
> downloads site. I am working on relatively high resolution
> structures with a number of alternate conformers for certain amino
> acids which I put in using the mac version of Coot 0.6-pre-1,
> something else I updated last week. However, when I now run refmac
> on a pdb file with two conformers for certain amino acids it seems
> that refmac doesn't recognise them and distorts the bond angles/
> lengths. I've checked the format of the pdb file outputted by coot
> and this seems normal (see below), which suggests to me that the new
> refmac doesn't like the A and B suffix on the residue name. Is this
> a known bug, and if so is there an easy fix?
>
> Thanks,
>
> Simon
>
>
> ATOM 860 N ASER A 107 -1.909 -4.393 -14.018 0.50
> 10.31 N
> ATOM 861 N BSER A 107 -1.942 -4.416 -14.064 0.50
> 8.93 N
> ATOM 862 CA ASER A 107 -0.633 -3.962 -14.010 0.50
> 6.64 C
> ATOM 863 CA BSER A 107 -0.669 -4.036 -13.974 0.50
> 5.74 C
> ATOM 864 CB ASER A 107 -0.549 -2.697 -13.710 0.50
> 7.45 C
> ATOM 865 CB BSER A 107 -0.505 -2.657 -13.639 0.50
> 6.94 C
> ATOM 866 OG ASER A 107 -0.877 -1.986 -12.787 0.50
> 16.90 O
> ATOM 867 OG BSER A 107 -0.869 -1.863 -14.924 0.50
> 3.17 O
> ATOM 868 C ASER A 107 -0.612 -4.590 -12.892 0.50
> 15.50 C
> ATOM 869 C BSER A 107 -0.533 -4.683 -12.889 0.50
> 12.17 C
> ATOM 870 O ASER A 107 -0.999 -5.055 -11.781 0.50
> 7.08 O
> ATOM 871 O BSER A 107 -1.003 -5.114 -11.813 0.50
> 7.22 O
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