Sorry my answers were confusing..
There are two problems. 1) When you finish data processing you should have
the correct point group, but you may not have the correct spacegroup (SG).
You will get an mtz file after processing, but may have to correct the SG
later.
Eg an orthorhombic point group will have all angles 90 degrees and 2-fold
symmetry around the a, b and c axis.
However the space group might be one of these 8. P 2 2 2, P 21 2 2 P 21 21
2, P 21 21 21, P2 21 2, P2 21 21, P 21 2 21 or P 2 2 21.
You can get an indicator of the SG from the systematic absences, but you
may only be sure of it when you have solved the MR search or experimental
phasing.
At that point you should go back and make sure the mtz from the data
processing has the correct SG in the header.
2) After any sort of manipulation your output amplitudes in the mtz file
will have been modified in some way.. This file will besuitable for reading
into COOT for model building.
You should NOT use this file for later refinement though .
Eleanor
On Mar 14 2012, Maheshwaran amanthakadavu wrote:
Dear crystallographers,
According *UMA RATU*'s mtz labellings,
*Vellieux Frederic *sir answered, output of the scalepack2mtz is
used as master mtz for all refining (refmac5) input(if i am wrong, sorry ).
am confused when Eleanor sir answered...
here my labellings !!!
scalepack2mtz ---- output_*1*.mtz
Phaser ----- output_*2*.mtz
Refmac5 --- output_*3*.mtz (output mtz from the refmac5 after first
refining, input is phaser output_*2 *.mtz )
As *Eleanor* sir told in second paragraph of his reply, i got other best
possible space group by running Phaser other than scalepack2mtz space group
( i mean output_*2*.mtz,C2221(Phaser) from output_*1*.mtz, C222
(scalepack2mtz) ) ..
Am right-now using output_*2*.mtz, Is it right to use output_*3*.mtz ?
and
from* Eleanor -- "*scalepack2mtz just run a jiffy to change it."
how to do? am using ccp4 6.0.0 in windows xp
Regards
VMW
On Thu, Mar 1, 2012 at 7:19 PM, Uma Ratu <rosiso2...@gmail.com> wrote:
Many thnaks for your input.
regards
Ros
On Wed, Feb 29, 2012 at 4:51 PM, Eleanor Dodson
<eleanor.dod...@york.ac.uk
> wrote:
mtz(1) will contain h k l F SIGF I SIGI and optionally F+ SIGF+ and F-
SIGF- This is your master file, providing the space group is correct
It may NOT have the correct space group however - MR searches may
select one space group from several possible ones. If the final SG is
different from the one specified after scalepack2mtz just run a jiffy
to change it.
e.g. mtzutils hklin1 scal1.mtz hklout scal2.mtz
symm SGname
end
then use scal2.mtz as your master..
The output from phaser will have the same F but after anisotropic
scaling. There will be other columns suitable for input to coot
the output from REFMAC will also give a scaled F plus extra columns .
Always start each new refinement with your master mtz as input..
coot will automatically select the best output from PHASER or REFMAC
to calculate maps. The columns FWT and PHWT are used to generate a
2mFobs-DFcalc map The columns DELFWT and PHDELWT generate a
mFobs-DFcalc map
Eleanor
On Feb 29 2012, Uma Ratu wrote:
Hello,
I have a question about .mtz files used in model building.
Here is how I did:
Diffraction data - HKL 2000: .sca
CCp4i: scalepack2mtz: .mtz (1)
Phaser: In: template pdb & .mtz(1)
Out: model .pdb(1) & .mtz(2)
Refmac5: model .pdb(2) & .mtz(3)
Here is the question:
1. Coot check and refinment: which mtz file shoudl I use?
2. With further refinemnt by refmac5, which mtz file should I use?
3. When I deposit data, which mtz file to use?
4. What is the difference between .mtz(1) and the .mtz files generated
from
"phaser" and "refmac"?
Thank you for advice
Ros
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
