On Fri, Dec 3, 2010 at 5:33 AM, Stephen Graham
I'm trying to use phenix.superpose_maps through the GUI to get superposed maps covering the same region of NCS-related chains A and B for a figure. I have used PDB Tools to split the model into two files with only chain A or chain B. However, when I run superpose_maps specifying the two individual chains for the input PDB files but the same mtz file for the map coefficients I only get one output map (I think it overwrites the output file...). Selected input from the generated .eff file is as follows:
saving CCP4 map to Native_refine_6_map_coeffs_superposed.ccp4 saving CCP4 map to Native_refine_6_map_coeffs_superposed.ccp4
A bug?
Definitely. Will fix this, but you could work around it for now a second copy of the MTZ file for now, and use that as the second input.
P.S. Incidentally, is there any reason you write both maps in a P1 box rather than putting map 2 on top of map 1 in the position of the first (reference) model? The latter would be more convenient as you can then re-use your carefully chosen pymol viewing matrices for all figures...
When Pavel and I were working on the map superpositioning we kept running into the problem of unit cell periodicity screwing up the result. Transforming everything into a P1 box with a large buffer around the molecules was the easiest way around the problem, but I agree that it's not ideal (it was written for a different project that needed results quickly). I think the CCP4 map format should allow us to do what you're asking, but I'm not sure if the maps API in CCTBX will - need to check this with Ralf. -Nat