Hmm - I dont understand that.
I ran structure idealisation on both examples and that tidies up the
geometry perfectly..
Are there some clashes with pre-existing water molecules or other
indicators in the log file that one conformation is suspect?(Look for
warnings..)
Eleanor
John Pascal wrote:
Hello All,
We are trying to refine ARG residues with two conformations in Refmac5, and the
refined atom positions in the output PDB file are all over the place, as if the
geometry restraints are not well defined.
We've tried several different formats for the input file, based on previous
postings to the bulletin board and the PDB standard (two examples below), but
the result is always the same.
We are using Refmac5 in CCP4 Suite 6.1.2, GUI 2.0.5 on Mac OSX.
We'd appreciate any suggestions. Thanks. -John
Examples of ARG format:
1)
ATOM 1472 N ARG A 1 -5.737 26.887 38.372 1.00 29.53 C N
ATOM 1473 CA ARG A 1 -5.445 25.560 37.882 1.00 30.24 C C
ATOM 1474 CB ARG A 1 -5.314 24.548 39.036 1.00 30.63 C C
ATOM 1475 CG ARG A 1 -5.426 23.052 38.627 1.00 34.81 C C
ATOM 1476 CD AARG A 1 -4.827 22.075 39.644 0.50 37.09 C C
ATOM 1477 CD BARG A 1 -4.301 22.419 39.279 0.50 37.09 C C
ATOM 1478 NE AARG A 1 -3.430 21.777 39.304 0.50 42.71 C N
ATOM 1479 NE BARG A 1 -4.482 21.902 40.627 0.50 42.71 C N
ATOM 1480 CZ AARG A 1 -2.998 20.868 38.402 0.50 44.91 C C
ATOM 1481 CZ BARG A 1 -3.648 22.142 41.638 0.50 44.91 C C
ATOM 1482 NH1AARG A 1 -3.841 20.117 37.678 0.50 45.20 C N
ATOM 1483 NH1BARG A 1 -2.584 22.912 41.464 0.50 45.20 C N
ATOM 1484 NH2AARG A 1 -1.688 20.715 38.210 0.50 44.99 C N
ATOM 1485 NH2BARG A 1 -3.878 21.619 42.831 0.50 44.99 C N
ATOM 1486 C ARG A 1 -6.518 25.176 36.830 1.00 29.97 C C
ATOM 1487 O ARG A 1 -7.675 25.501 36.971 1.00 31.02 C O
2)
ATOM 44 N AARG A 1 26.671 62.112 46.990 0.50 30.13 A N
ATOM 45 CA AARG A 1 26.970 63.346 47.667 0.50 30.65 A C
ATOM 46 CB AARG A 1 27.172 64.495 46.676 0.50 31.07 A C
ATOM 47 CG AARG A 1 27.152 65.897 47.322 0.50 34.20 A C
ATOM 48 CD AARG A 1 27.993 66.976 46.599 0.50 37.16 A C
ATOM 49 NE AARG A 1 27.726 67.425 45.342 0.50 42.06 A N
ATOM 50 CZ AARG A 1 28.315 67.639 44.168 0.50 44.78 A C
ATOM 51 NH1AARG A 1 29.525 67.160 43.918 0.50 45.37 A N
ATOM 52 NH2AARG A 1 27.690 68.340 43.240 0.50 45.67 A N
ATOM 53 C AARG A 1 25.839 63.640 48.622 0.50 30.37 A C
ATOM 54 O AARG A 1 24.690 63.377 48.340 0.50 31.24 A O
ATOM 55 N BARG A 1 26.667 62.080 47.010 0.50 30.13 A N
ATOM 56 CA BARG A 1 26.921 63.329 47.640 0.50 30.65 A C
ATOM 57 CB BARG A 1 27.108 64.390 46.581 0.50 31.07 A C
ATOM 58 CG BARG A 1 27.138 65.756 47.103 0.50 34.20 A C
ATOM 59 CD BARG A 1 28.447 66.452 46.933 0.50 37.16 A C
ATOM 60 NE BARG A 1 28.377 67.657 47.707 0.50 42.06 A N
ATOM 61 CZ BARG A 1 29.349 68.269 48.373 0.50 44.78 A C
ATOM 62 NH1BARG A 1 30.572 67.836 48.373 0.50 45.37 A N
ATOM 63 NH2BARG A 1 29.066 69.368 49.034 0.50 45.67 A N
ATOM 64 C BARG A 1 25.822 63.636 48.638 0.50 30.37 A C
ATOM 65 O BARG A 1 24.698 63.372 48.403 0.50 31.24 A O
John Pascal, PhD
Thomas Jefferson University
Department of Biochemistry & Molecular Biology
233 South 10th Street, BLSB 804
Philadelphia, Pennsylvania 19107
ph 215.503.4596
fx 215.923.2117
