Re: [ccp4bb] Fast,medium,slow axis do not match

[Kevin Cowtan]

You could feed *both* maps through mapmask with AXIS X Y Z to convert 
them to the same axis order.


You may also have a problem with the maps having different XYZLIM 
ranges. In that case, using XYZLIM MATCH on the second run of mapmask to 
match the second map to the first should fix it.


Kevin

Hailiang Zhang wrote:

Hi there,

I was generating the atomic mask using ccpr-sfall, and generating real
maps using ccp4-fft, and then ccp4-overlap these maps to calculate the cc
values. However, ccp4-overlapmap frequently complaints that the
Fast,medium,slow axis do not match for these maps. Following are the
script I was using, and thanks for any advice (I can't manually change the
keywords values one by one since everything needs automated):


sfall xyzin ${OUTTMPDIR}${PDB}-Bsmall-0B.pdb \
  mapout ${OUTTMPDIR}${PDB}-Bsmall-mask.map\
 END-sfall
TITL Toxd Atom map from final coordinates
MODE ATMMAP RESMOD
GRID ${GRID}
SYMM ${spcgrp}
FORM NGAU 5
END
END-sfall

...



fft ${OUTLOGDIR}${PDB}-0B-fft.log\
hklin ${OUTTMPDIR}${PDB}-0B.mtz \
mapout ${OUTTMPDIR}${PDB}-0B.map\
 END-fft
TITL data_toxd
GRID ${GRID}
XYZLIM  ASU
RESO 100.0 ${resolution}
LABI F1=FOBS PHI=PHIFMODEL
END
END-fft
*



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Re: [ccp4bb] Fast,medium,slow axis do not match

[Eleanor Dodson]

Alternatively you can force the fft to generate a map with the sfall 
axiis order (sfall has a fixed axis order governed by the spacegroup)

From the fft documentation
You can set

AXIS fast medium slow

Eleanor

Kevin Cowtan wrote:
You could feed *both* maps through mapmask with AXIS X Y Z to convert 
them to the same axis order.


You may also have a problem with the maps having different XYZLIM 
ranges. In that case, using XYZLIM MATCH on the second run of mapmask to 
match the second map to the first should fix it.


Kevin

Hailiang Zhang wrote:

Hi there,

I was generating the atomic mask using ccpr-sfall, and generating real
maps using ccp4-fft, and then ccp4-overlap these maps to calculate the cc
values. However, ccp4-overlapmap frequently complaints that the
Fast,medium,slow axis do not match for these maps. Following are the
script I was using, and thanks for any advice (I can't manually change 
the

keywords values one by one since everything needs automated):


sfall xyzin ${OUTTMPDIR}${PDB}-Bsmall-0B.pdb \
  mapout ${OUTTMPDIR}${PDB}-Bsmall-mask.map\
 END-sfall
TITL Toxd Atom map from final coordinates
MODE ATMMAP RESMOD
GRID ${GRID}
SYMM ${spcgrp}
FORM NGAU 5
END
END-sfall

...



fft ${OUTLOGDIR}${PDB}-0B-fft.log\
hklin ${OUTTMPDIR}${PDB}-0B.mtz \
mapout ${OUTTMPDIR}${PDB}-0B.map\
 END-fft
TITL data_toxd
GRID ${GRID}
XYZLIM  ASU
RESO 100.0 ${resolution}
LABI F1=FOBS PHI=PHIFMODEL
END
END-fft
*

[ccp4bb] Fast,medium,slow axis do not match

[Hailiang Zhang]

Hi there,

I was generating the atomic mask using ccpr-sfall, and generating real
maps using ccp4-fft, and then ccp4-overlap these maps to calculate the cc
values. However, ccp4-overlapmap frequently complaints that the
Fast,medium,slow axis do not match for these maps. Following are the
script I was using, and thanks for any advice (I can't manually change the
keywords values one by one since everything needs automated):


sfall xyzin ${OUTTMPDIR}${PDB}-Bsmall-0B.pdb \
  mapout ${OUTTMPDIR}${PDB}-Bsmall-mask.map\
 END-sfall
TITL Toxd Atom map from final coordinates
MODE ATMMAP RESMOD
GRID ${GRID}
SYMM ${spcgrp}
FORM NGAU 5
END
END-sfall

...



fft ${OUTLOGDIR}${PDB}-0B-fft.log\
hklin ${OUTTMPDIR}${PDB}-0B.mtz \
mapout ${OUTTMPDIR}${PDB}-0B.map\
 END-fft
TITL data_toxd
GRID ${GRID}
XYZLIM  ASU
RESO 100.0 ${resolution}
LABI F1=FOBS PHI=PHIFMODEL
END
END-fft
*