On Fri, 2010-01-29 at 00:14 -0500, Xun Lu wrote: > So, how can I tell Refmac not to sacrifice the geometry of DNA > to fit my poor density? Or, how to fix the DNA (just like in CNS)? > Anyone could share their experience and tricks about dealing with > DNA? >
Xun, I needed once to restrain the proper Watson-Crick pairing in the structure where density was poor and DNA had the tendency to blow up near the sticky ends. Things may have changed since , but at the time I followed Garib's suggestion to use external restraints file. I attach the refmac command file and external restraints that I used, review and edit to your needs. HTH, Ed. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
refmac.in
Description: application/shellscript
external distance first chain D residue 23 atom O4 second chain C residue 23 atom N6 value 2.95 sigma 0.01 symm Y external distance first chain D residue 23 atom N3 second chain C residue 23 atom N1 value 2.82 sigma 0.01 symm Y external distance first chain D residue 23 atom O4 second chain C residue 23 atom N1 value 3.63 sigma 0.01 symm Y external distance first chain D residue 23 atom O2 second chain C residue 23 atom N6 value 5.40 sigma 0.01 symm Y external distance first chain D residue 22 atom O6 second chain C residue 1 atom N4 value 2.91 sigma 0.01 external distance first chain D residue 22 atom N1 second chain C residue 1 atom N3 value 2.95 sigma 0.01 external distance first chain D residue 22 atom N2 second chain C residue 1 atom O2 value 2.86 sigma 0.01 external distance first chain D residue 22 atom N2 second chain C residue 1 atom N3 value 3.65 sigma 0.01 external distance first chain D residue 22 atom O6 second chain C residue 1 atom O2 value 5.42 sigma 0.01 external distance first chain D residue 21 atom O4 second chain C residue 2 atom N6 value 2.95 sigma 0.01 external distance first chain D residue 21 atom N3 second chain C residue 2 atom N1 value 2.82 sigma 0.01 external distance first chain D residue 21 atom O4 second chain C residue 2 atom N1 value 3.63 sigma 0.01 external distance first chain D residue 21 atom O2 second chain C residue 2 atom N6 value 5.40 sigma 0.01 external distance first chain D residue 20 atom N4 second chain C residue 3 atom O6 value 2.91 sigma 0.01 external distance first chain D residue 20 atom N3 second chain C residue 3 atom N1 value 2.95 sigma 0.01 external distance first chain D residue 20 atom O2 second chain C residue 3 atom N2 value 2.86 sigma 0.01 external distance first chain D residue 20 atom N3 second chain C residue 3 atom N2 value 3.65 sigma 0.01 external distance first chain D residue 20 atom O2 second chain C residue 3 atom O6 value 5.42 sigma 0.01 external distance first chain D residue 19 atom O6 second chain C residue 4 atom N4 value 2.91 sigma 0.01 external distance first chain D residue 19 atom N1 second chain C residue 4 atom N3 value 2.95 sigma 0.01 external distance first chain D residue 19 atom N2 second chain C residue 4 atom O2 value 2.86 sigma 0.01 external distance first chain D residue 19 atom N2 second chain C residue 4 atom N3 value 3.65 sigma 0.01 external distance first chain D residue 19 atom O6 second chain C residue 4 atom O2 value 5.42 sigma 0.01 external distance first chain D residue 18 atom N6 second chain C residue 5 atom O4 value 2.95 sigma 0.01 external distance first chain D residue 18 atom N1 second chain C residue 5 atom N3 value 2.82 sigma 0.01 external distance first chain D residue 18 atom N1 second chain C residue 5 atom O4 value 3.63 sigma 0.01 external distance first chain D residue 18 atom N6 second chain C residue 5 atom O2 value 5.40 sigma 0.01 external distance first chain D residue 17 atom O6 second chain C residue 6 atom N4 value 2.91 sigma 0.01 external distance first chain D residue 17 atom N1 second chain C residue 6 atom N3 value 2.95 sigma 0.01 external distance first chain D residue 17 atom N2 second chain C residue 6 atom O2 value 2.86 sigma 0.01 external distance first chain D residue 17 atom N2 second chain C residue 6 atom N3 value 3.65 sigma 0.01 external distance first chain D residue 17 atom O6 second chain C residue 6 atom O2 value 5.42 sigma 0.01 external distance first chain D residue 16 atom N6 second chain C residue 7 atom O4 value 2.95 sigma 0.01 external distance first chain D residue 16 atom N1 second chain C residue 7 atom N3 value 2.82 sigma 0.01 external distance first chain D residue 16 atom N1 second chain C residue 7 atom O4 value 3.63 sigma 0.01 external distance first chain D residue 16 atom N6 second chain C residue 7 atom O2 value 5.40 sigma 0.01 external distance first chain D residue 15 atom N4 second chain C residue 8 atom O6 value 2.91 sigma 0.01 external distance first chain D residue 15 atom N3 second chain C residue 8 atom N1 value 2.95 sigma 0.01 external distance first chain D residue 15 atom O2 second chain C residue 8 atom N2 value 2.86 sigma 0.01 external distance first chain D residue 15 atom N3 second chain C residue 8 atom N2 value 3.65 sigma 0.01 external distance first chain D residue 15 atom O2 second chain C residue 8 atom O6 value 5.42 sigma 0.01 external distance first chain D residue 14 atom N6 second chain C residue 9 atom O4 value 2.95 sigma 0.01 external distance first chain D residue 14 atom N1 second chain C residue 9 atom N3 value 2.82 sigma 0.01 external distance first chain D residue 14 atom N1 second chain C residue 9 atom O4 value 3.63 sigma 0.01 external distance first chain D residue 14 atom N6 second chain C residue 9 atom O2 value 5.40 sigma 0.01 external distance first chain D residue 13 atom O4 second chain C residue 10 atom N6 value 2.95 sigma 0.01 external distance first chain D residue 13 atom N3 second chain C residue 10 atom N1 value 2.82 sigma 0.01 external distance first chain D residue 13 atom O4 second chain C residue 10 atom N1 value 3.63 sigma 0.01 external distance first chain D residue 13 atom O2 second chain C residue 10 atom N6 value 5.40 sigma 0.01 external distance first chain D residue 12 atom O6 second chain C residue 11 atom N4 value 2.91 sigma 0.01 external distance first chain D residue 12 atom N1 second chain C residue 11 atom N3 value 2.95 sigma 0.01 external distance first chain D residue 12 atom N2 second chain C residue 11 atom O2 value 2.86 sigma 0.01 external distance first chain D residue 12 atom N2 second chain C residue 11 atom N3 value 3.65 sigma 0.01 external distance first chain D residue 12 atom O6 second chain C residue 11 atom O2 value 5.42 sigma 0.01 # Pair mismatch: D 11:D1P--- G:C 12 external distance first chain D residue 10 atom N6 second chain C residue 13 atom O4 value 2.95 sigma 0.01 external distance first chain D residue 10 atom N1 second chain C residue 13 atom N3 value 2.82 sigma 0.01 external distance first chain D residue 10 atom N1 second chain C residue 13 atom O4 value 3.63 sigma 0.01 external distance first chain D residue 10 atom N6 second chain C residue 13 atom O2 value 5.40 sigma 0.01 external distance first chain D residue 9 atom N4 second chain C residue 14 atom O6 value 2.91 sigma 0.01 external distance first chain D residue 9 atom N3 second chain C residue 14 atom N1 value 2.95 sigma 0.01 external distance first chain D residue 9 atom O2 second chain C residue 14 atom N2 value 2.86 sigma 0.01 external distance first chain D residue 9 atom N3 second chain C residue 14 atom N2 value 3.65 sigma 0.01 external distance first chain D residue 9 atom O2 second chain C residue 14 atom O6 value 5.42 sigma 0.01 external distance first chain D residue 8 atom O4 second chain C residue 15 atom N6 value 2.95 sigma 0.01 external distance first chain D residue 8 atom N3 second chain C residue 15 atom N1 value 2.82 sigma 0.01 external distance first chain D residue 8 atom O4 second chain C residue 15 atom N1 value 3.63 sigma 0.01 external distance first chain D residue 8 atom O2 second chain C residue 15 atom N6 value 5.40 sigma 0.01 external distance first chain D residue 7 atom N4 second chain C residue 16 atom O6 value 2.91 sigma 0.01 external distance first chain D residue 7 atom N3 second chain C residue 16 atom N1 value 2.95 sigma 0.01 external distance first chain D residue 7 atom O2 second chain C residue 16 atom N2 value 2.86 sigma 0.01 external distance first chain D residue 7 atom N3 second chain C residue 16 atom N2 value 3.65 sigma 0.01 external distance first chain D residue 7 atom O2 second chain C residue 16 atom O6 value 5.42 sigma 0.01 external distance first chain D residue 6 atom O6 second chain C residue 17 atom N4 value 2.91 sigma 0.01 external distance first chain D residue 6 atom N1 second chain C residue 17 atom N3 value 2.95 sigma 0.01 external distance first chain D residue 6 atom N2 second chain C residue 17 atom O2 value 2.86 sigma 0.01 external distance first chain D residue 6 atom N2 second chain C residue 17 atom N3 value 3.65 sigma 0.01 external distance first chain D residue 6 atom O6 second chain C residue 17 atom O2 value 5.42 sigma 0.01 external distance first chain D residue 5 atom O4 second chain C residue 18 atom N6 value 2.95 sigma 0.01 external distance first chain D residue 5 atom N3 second chain C residue 18 atom N1 value 2.82 sigma 0.01 external distance first chain D residue 5 atom O4 second chain C residue 18 atom N1 value 3.63 sigma 0.01 external distance first chain D residue 5 atom O2 second chain C residue 18 atom N6 value 5.40 sigma 0.01 external distance first chain D residue 4 atom N4 second chain C residue 19 atom O6 value 2.91 sigma 0.01 external distance first chain D residue 4 atom N3 second chain C residue 19 atom N1 value 2.95 sigma 0.01 external distance first chain D residue 4 atom O2 second chain C residue 19 atom N2 value 2.86 sigma 0.01 external distance first chain D residue 4 atom N3 second chain C residue 19 atom N2 value 3.65 sigma 0.01 external distance first chain D residue 4 atom O2 second chain C residue 19 atom O6 value 5.42 sigma 0.01 external distance first chain D residue 3 atom N6 second chain C residue 20 atom O4 value 2.95 sigma 0.01 external distance first chain D residue 3 atom N1 second chain C residue 20 atom N3 value 2.82 sigma 0.01 external distance first chain D residue 3 atom N1 second chain C residue 20 atom O4 value 3.63 sigma 0.01 external distance first chain D residue 3 atom N6 second chain C residue 20 atom O2 value 5.40 sigma 0.01 external distance first chain D residue 2 atom N4 second chain C residue 21 atom O6 value 2.91 sigma 0.01 external distance first chain D residue 2 atom N3 second chain C residue 21 atom N1 value 2.95 sigma 0.01 external distance first chain D residue 2 atom O2 second chain C residue 21 atom N2 value 2.86 sigma 0.01 external distance first chain D residue 2 atom N3 second chain C residue 21 atom N2 value 3.65 sigma 0.01 external distance first chain D residue 2 atom O2 second chain C residue 21 atom O6 value 5.42 sigma 0.01 external distance first chain D residue 1 atom N4 second chain C residue 22 atom O6 value 2.91 sigma 0.01 external distance first chain D residue 1 atom N3 second chain C residue 22 atom N1 value 2.95 sigma 0.01 external distance first chain D residue 1 atom O2 second chain C residue 22 atom N2 value 2.86 sigma 0.01 external distance first chain D residue 1 atom N3 second chain C residue 22 atom N2 value 3.65 sigma 0.01 external distance first chain D residue 1 atom O2 second chain C residue 22 atom O6 value 5.42 sigma 0.01
