Re: [ccp4bb] Expanding p4212 coordinates to p1
Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.chwrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
Re: [ccp4bb] Expanding p4212 coordinates to p1
I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
Re: [ccp4bb] Expanding p4212 coordinates to p1
Apologies - I didn't notice the plane group.. Although I think if the sym ops are correctly listed in the P4121 file they will just be applied as given.. Eleanor On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote: I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
Re: [ccp4bb] Expanding p4212 coordinates to p1
'echo symm x,y | cad' gives: Data line--- symm x,y **SYMMETRY OPERATOR ERROR** Error in interpreting symop X,Y I. On 12 April 2012 12:03, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Apologies - I didn't notice the plane group.. Although I think if the sym ops are correctly listed in the P4121 file they will just be applied as given.. Eleanor On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote: I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
Re: [ccp4bb] Expanding p4212 coordinates to p1
On 2nd thoughts I guess you could do it in a space group that's a supergroup of the plane group say with all l and all z = 0. Then you could use symm x,y,z and it would just ignore the z components (I think?). I. On 12 April 2012 12:11, Ian Tickle ianj...@gmail.com wrote: 'echo symm x,y | cad' gives: Data line--- symm x,y **SYMMETRY OPERATOR ERROR** Error in interpreting symop X,Y I. On 12 April 2012 12:03, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Apologies - I didn't notice the plane group.. Although I think if the sym ops are correctly listed in the P4121 file they will just be applied as given.. Eleanor On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote: I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
Re: [ccp4bb] Expanding p4212 coordinates to p1
I am confused by the discussion on this message. Although it says plane group I assume it really is a normal 3D tetragonal space group, P42(1)2 So Eleanor's suggestion should work and sftools expand command will do the job as well. Bart On 12-04-12 05:03 AM, Eleanor Dodson wrote: Apologies - I didn't notice the plane group.. Although I think if the sym ops are correctly listed in the P4121 file they will just be applied as given.. Eleanor On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote: I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and "generate chains by symmetry operators" eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with "expand 1" to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command "expand 1", and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA,
Re: [ccp4bb] Expanding p4212 coordinates to p1
Yes I was also confused by the fact that P4212 is obviously a space group (upper case 'P') whereas p4 and p1 are plane groups (lower case 'p'), as stated. Not sure what 'p2121' is though, I assumed it was somehow related to the p2gg plane group (no 8). Also there's no plane group 'p6212', but then there's no space group 'P6212' either. Perhaps the original poster could clarify and take care with his P's and p's? Cheers -- Ian On 12 April 2012 16:51, Bart Hazes bha...@ualberta.ca wrote: I am confused by the discussion on this message. Although it says plane group I assume it really is a normal 3D tetragonal space group, P42(1)2 So Eleanor's suggestion should work and sftools expand command will do the job as well. Bart On 12-04-12 05:03 AM, Eleanor Dodson wrote: Apologies - I didn't notice the plane group.. Although I think if the sym ops are correctly listed in the P4121 file they will just be applied as given.. Eleanor On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote: I didn't realise the CCP4 suite could handle the plane groups: where are they listed (they're not in symop.lib or syminfo.lib)? Or are they doing some clever projections of the space groups? Cheers -- Ian On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Cad will do this correctly Reflection utilitied - merge mtz ( rather confusing job title - sorry..) mtz in - the P4121.mtz data Output - P41212-ext.mtz Defne mtz output Select define limit for refl;action by Laue code select P1 then you will get a list of all P1 reflections with phases correctly modified. If you really want to work in P1 you will need to change the space group in P41212-ext.mtz Easiest way is mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz SYMM P1 end DONT change the G of P41212.mtz before doing the extension - the program needs the P41212 sym ops to change the phases correctly.. If you want the coordinates extended too use pdbset to get a P1 set of cds.. (Coordinate utilities Edit pdb select pdbset and generate chains by symmetry operators eleanor Eleanor On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch wrote: Hi Everybody, I am working in a P4212 plane group, which is a p4 symmetric structure with a screw axis in addition. My map has in the unit cell two 4-fold symmetric structures, one if which is upside-down with respect to the other one. If using expand in sftools, then the resulting map is p4 symmetrized in the center between two p4-symmetric structures, which is wrong. This is probably the phase origin problem referred to here: http://www.ccp4.ac.uk/dist/html/sftools.html#expand Would anybody have a suggestion how I can expand the p4212 MTZ file to full p1, but with properly respecting the symmetry phase origin? My illiterate guess would be to either 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then use sftools with expand 1 to create the full reflection sets in p1; then shift back by (180.0;0.0); or 2) use sftools with the command expand 1, and then modify (invert?) the phases of the reflections in the quadrants that have wrong phases. In option 1) I am not sure if it is possible to shift phase origin, while staying in p4212 symmetry. How could I do that? In option 2) I would probably get into deep water the next time I work with another symmetry, like p6212, or p2121, where I would have to deal not with quadrants but with triangles of 60deg angle? Any suggestions would be highly appreciated. All the best, Henning. Henning Stahlberg, PhD Prof. for Structural Biology, C-CINA, Biozentrum, University Basel Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland http://c-cina.org | Tel. +41-61-387 32 62
Re: [ccp4bb] Expanding p4212 coordinates to p1
Hi,
I was referring to P42(1)2, which is the CCP4 symmetry number 90.
I am working on 2D membrane protein crystals and cryo-electron microscopy
images of these, where I initially deal with two-dimensional projection images,
which are eventually merged into a 3D dataset. Therefore my sloppy formulation.
Thanks for the suggestions from several people on this list.
What I am doing now, and what works well, is:
\rm -f SCRATCH/merge3Dref-clean.mtz
#
${bin_ccp4}/sftools eof
read SCRATCH/merge3Dref.mtz
sort h k l
set spacegroup
${CCP4_SYM}
select phaerr
select invert
purge
y
write SCRATCH/merge3Dref-clean.mtz
quit
eof
#
\rm -f SCRATCH/merge3Dref-clean-p1.mtz
#
${bin_ccp4}/cad hklin1 SCRATCH/merge3Dref-clean.mtz hklout
SCRATCH/merge3Dref-clean-p1.mtz eof
reso overall 1 1
outlim spacegroup 1
labin file 1 all
end
eof
#
\rm -f merge3Dref.mtz
#
${bin_ccp4}/sftools eof
read SCRATCH/merge3Dref-clean-p1.mtz
sort h k l
set spacegroup
1
reduce matrix 1 0 0 0 1 0 0 0 1
write merge3Dref.mtz
quit
eof
#
All the best,
Henning.
On Apr 12, 2012, at 6:10 PM, Ian Tickle wrote:
Yes I was also confused by the fact that P4212 is obviously a space
group (upper case 'P') whereas p4 and p1 are plane groups (lower case
'p'), as stated. Not sure what 'p2121' is though, I assumed it was
somehow related to the p2gg plane group (no 8). Also there's no plane
group 'p6212', but then there's no space group 'P6212' either.
Perhaps the original poster could clarify and take care with his P's and p's?
Cheers
-- Ian
On 12 April 2012 16:51, Bart Hazes bha...@ualberta.ca wrote:
I am confused by the discussion on this message. Although it says plane
group I assume it really is a normal 3D tetragonal space group, P42(1)2
So Eleanor's suggestion should work and sftools expand command will do the
job as well.
Bart
On 12-04-12 05:03 AM, Eleanor Dodson wrote:
Apologies - I didn't notice the plane group..
Although I think if the sym ops are correctly listed in the P4121 file they
will just be applied as given..
Eleanor
On 12 April 2012 11:58, Ian Tickle ianj...@gmail.com wrote:
I didn't realise the CCP4 suite could handle the plane groups: where
are they listed (they're not in symop.lib or syminfo.lib)? Or are
they doing some clever projections of the space groups?
Cheers
-- Ian
On 12 April 2012 11:48, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
Cad will do this correctly
Reflection utilitied - merge mtz ( rather confusing job title - sorry..)
mtz in - the P4121.mtz data
Output - P41212-ext.mtz
Defne mtz output
Select define limit for refl;action by Laue code select P1
then you will get a list of all P1 reflections with phases correctly
modified.
If you really want to work in P1 you will need to change the space group
in
P41212-ext.mtz
Easiest way is
mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz
SYMM P1
end
DONT change the G of P41212.mtz before doing the extension - the program
needs the P41212 sym ops to change the phases correctly..
If you want the coordinates extended too
use pdbset to get a P1 set of cds.. (Coordinate utilities
Edit pdb
select pdbset and generate chains by symmetry operators
eleanor
Eleanor
On 12 April 2012 06:51, Henning Stahlberg henning.stahlb...@unibas.ch
wrote:
Hi Everybody,
I am working in a P4212 plane group, which is a p4 symmetric structure
with a screw axis in addition. My map has in the unit cell two 4-fold
symmetric structures, one if which is upside-down with respect to the
other
one. If using expand in sftools, then the resulting map is p4
symmetrized
in the center between two p4-symmetric structures, which is wrong. This
is
probably the phase origin problem referred to here:
http://www.ccp4.ac.uk/dist/html/sftools.html#expand
Would anybody have a suggestion how I can expand the p4212 MTZ file to
full p1, but with properly respecting the symmetry phase origin?
My illiterate guess would be to either
1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then
use
sftools with expand 1 to create the full reflection sets in p1; then
shift
back by (180.0;0.0); or
2) use sftools with the command expand 1, and then modify (invert?)
the
phases of the reflections in the quadrants that have wrong phases.
In option 1) I am not sure if it is possible to shift phase origin,
while
staying in p4212 symmetry. How could I do that?
In option 2) I would probably get into deep water the next time I work
with another symmetry, like p6212, or p2121, where I would have to deal
not
with quadrants but with triangles of 60deg angle?
Any suggestions would be highly appreciated.
All the best,
Henning.
Henning Stahlberg, PhD
Prof. for Structural Biology, C-CINA, Biozentrum, University Basel
Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland
http://c-cina.org | Tel. +41-61-387 32 62
