[phenixbb] Issue with phenix.superpose_maps

Stephen Graham scg34 at cam.ac.uk
Fri Dec 3 05:33:08 PST 2010

Hi all,

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:

  input_files {
    map_1 = "/home/stepheng/blah/Native_refine_6_map_coeffs.mtz"
    labels_1 = 2FOFCWT,PH2FOFCWT
    map_2 = "/home/stepheng/blah/Native_refine_6_map_coeffs.mtz"
    labels_2 = 2FOFCWT,PH2FOFCWT
    pdb_1 = "/home/stepheng/blah/Native_refine_6_chainA.pdb"
    d_min_1 = None
    pdb_2 = "/home/stepheng/blah/Native_refine_6_chainB.pdb"
    d_min_2 = None
    output_dir = "/home/stepheng/blah"

And the end of the output is as follows:

    saving CCP4 map to Native_refine_6_map_coeffs_superposed.ccp4
Wrote Native_refine_6_chainA_superposed.pdb
Wrote Native_refine_6_map_coeffs_superposed.ccp4
    saving CCP4 map to Native_refine_6_map_coeffs_superposed.ccp4
Wrote Native_refine_6_chainB_superposed.pdb
Wrote Native_refine_6_map_coeffs_superposed.ccp4

A bug?


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

Dr Stephen Graham
1851 Research Fellow
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
Addenbrooke's Hospital, Hills Road
Cambridge, CB2 0XY, UK
Phone: +44 1223 762 638

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