Hi everyone, I’m having trouble aligning a map generated by PanDDA (event map) with its corresponding PDB file in PyMOL. The map is in `native.ccp4` format and it loads correctly in Coot, aligning perfectly with the PDB. However, when I load the same files in PyMOL, the map appears misaligned with the structure.
### What I've Tried: 1. **Loading in Coot:** The map and PDB align correctly in Coot. 2. **Using `phenix.map_box`:** ```bash phenix.map_box map_file=Entry-A12A-event_1_1-BDC_0.24_map.native.ccp4 pdb_file=Entry-A12A.pdb ``` This generates a new map, but it still appears misaligned in PyMOL. Has anyone faced similar issues with PanDDA maps in PyMOL? Any suggestions for ensuring the map aligns correctly in PyMOL? Any help or suggestions would be greatly appreciated, as I need charming figures for publication. Thank you a lot! ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
