CCP4 pdbset is very good for this. Find the symops in $CCP4/lib/data/symop.lib and use symgen and chain commands to create each with a different chain ID. The six-fold screw is generated by: X,Y,Z -Y,X-Y,2/3+Z Y-X,-X,1/3+Z -X,-Y,1/2+Z Y,Y-X,1/6+Z X-Y,X,5/6+Z X,Y,1+Z
but the two-fold defines a dimer which is probably involved in the helix, so you might want to include all 12 symops plus unit cell translation along Z eab >>> Smith Liu <smith_liu...@163.com> 12/09/16 8:03 AM >>> Dear All, I mean if the radius set in the Coot "Cell Symmetry" was too small, not enough monomers (less than 6) can be displayed to show the "continuous helix with a six-fold screw axis". If the radius was too large, as for the "continuous helix with a six-fold screw axis" can be regarded as a "rod", too large radius will lead to show several rods in one window. But with the Coot window, it cannot distinguish which monomer was from which rod. Thus I cannot identify 6 monomers forming the single rod, i.e., a "continuous helix with a six-fold screw axis". Can anyone explain in this situation how can I identify the 6 monomers in the Coot "Cell and SYmmetry" windows forming a single "continuous helix with a six-fold screw axis"? Smith -------- Forwarding messages -------- From: "Smith Lee" <00000459ef8548d5-dmarc-requ...@jiscmail.ac.uk> Date: 2016-12-09 18:12:20 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] on Cell & Symmetry in coot Dear All, There is a pdb, once opended in coot, it was a monomer (space group P 65 2 2 ). But in the correspondence paper, it writes, "the subunits form a continuous helix with a six-fold screw axis". I have tried to view with Coot the "six-fold screw axis" formed by 6 monomers. But in the "Cell & Symmetry" in Coot, if the radius is small, 6 monomers cannot be shown. If I increase the radius, more than 6 monomers would occur in the window, and it can hardly distinguish the 6 monomers forming the "six-fold screw axis". In this situation, will you please let me know how to use Coot to identify the 6 monomers forming the "six-fold screw axis"? In addition, suppose 6 monomers forming the "six-fold screw axis" have been identified in Coot, in order to save the pdb of each monomer, I need to click each monomer in mouse, then by "Save symmetry coordinates" to save the pdb of each monomer, right? I am looking forward to getting your reply. Smith
