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
