Dear Xplor-NIH Development Team, Thank you very much for creating and maintaining such an excellent program. I am a graduate student in the Department of Life Sciences at Seoul National University, where I am investigating the structural evolution of fibrous proteins. I am now preparing to perform fiber diffraction refinement using Xplor-NIH, and although I have followed the examples provided on your website, I remain unsure whether my particular system can be treated in the same way. I would be grateful if you could help me by answering the following two questions:
1. *Helix arrangement and NCS settings* My system contains a strongly crystalline 3/1 helix (three residues per pitch), and unit-cell indexing has been determined as an orthorhombic cell with parameters 23 Å, 10 Å, 8.26 Å, 90°, 90°, 90°. Within each cell, two antiparallel helices are present. In the ncs strict protocol, only translations along Z appear to be enforced. However, I would like to include both helices in a single PDB file and simply replicate (extend) them along the Z axis—without applying any additional rotations—since each residue is already rotated by 120° in the input file. Which Xplor-NIH INP parameter(s) should I use to achieve this “pure Z-axis expansion” of all helices in the unit cell? Alternatively, is there a way within Xplor-NIH to translate the helices along the X and Y axes and enforce their antiparallel symmetry prior to performing fiber diffraction refinement? 2. *Order of intensity data in the layer-line file* In a line such as LAYER LINE 0 HIGHEST R 477 LOWEST R 1 should the corresponding intensity values be listed in order from highest R → lowest R, or from lowest R → highest R? Your guidance on these points would be extremely helpful for progressing with my refinement. Thank you in advance for your time and assistance. Sincerely, Jeong Jun Lee Graduate Student, Department of Life Sciences Seoul National University ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
