[PyMOL] why does coordinates not overlap with map

2022-04-29 Thread sunyeping via PyMOL-users
Dear pymol users, I have a coordinate file (pdb) and a map file (mtz), and I want to make a image that shows both the coordinate and the map. I generate a .map.ccp4 file using fft in CCP4 program. However, when I open the pdb file and the .map.ccp4 in pymol, I find the coordinates are out of th

[PyMOL] handling of multiple files in batch mode

2022-04-29 Thread Enrico Martinez
Dear Pymol Users! My Pymol batch script loads all pdb filles from the output directory split states and saves the pse session pymol "${output}"/*.pdb -c -d " from pymol import cmd #cmd.load('${output}/*.pdb') cmd.set('grid_mode','1') cmd.orient() cmd.bg_color('white') cmd.show('sticks'