Dear all, Thank you for the suggestions regarding cartoon problem that I posted on bulletin board. The problem was due to the separate segID put out after the phenix refinement. According to the PDB format, if I am not wrong, column number 73 should be blank which is followed by element name. But phenix puts segID in that column. During the refinement it has assigned the segID in column 22 througout where as in other column there were missing in some cases. Because of that I had seen a break in column in pymol. The suggestion given by Ingo P. Korndoerfer to assign the segID to those missing ones helped to close the gap. And also suggestion by Warren DeLano "set retain_order and rebuild" did the trick.
Presence of segID in column 73 appears to be off the PDB format. But I would like to know why then phenix.refine adds that additional column in the pdb file? Thanking you Madoori pramod
