Re: [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-31 Thread Eleanor Dodson
Is the R factor for the best solution really > 40% - if so there must be some major errors to correct. Eleanor On Fri, 31 Jul 2020 at 11:08, John R Helliwell wrote: > Dear Rafal, > The difference map you show in your attachment has an echo of the main > structure sort of look. So, I suggest you

Re: [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-31 Thread John R Helliwell
Dear Rafal, The difference map you show in your attachment has an echo of the main structure sort of look. So, I suggest you examine your diffraction images specifically looking out for a supercell of weak intensity spots, not picked up by the autoindexing, between the main lattice of

Re: [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-30 Thread Tim Gruene
Dear Rafal, with such a small molecule, and if you really have 1.0A resolution, you should be able to solve the structure by direct methods with shelxt. By default, shelxt searches all space groups in the Laue group. The output will not be very practical to assign residue, etc. but at least it

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-30 Thread Schreuder, Herman /DE
-Ursprüngliche Nachricht- Von: CCP4 bulletin board Im Auftrag von Rafal Dolot Gesendet: Donnerstag, 30. Juli 2020 14:06 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] Problems with refinement of nucleic acid structure EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk

Re: [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-30 Thread Rafal Dolot
Dear all, Thank you for the response. I will try to explain it more precisely. The molecule of interest is a duplex with 9 nt length, but is paired on the length of eight bases, with overhangs at ends. Molecules form a parallel strings across the crystal lattice, parallel to C-axis, because