This sentence in my previous posting may or may not be correct technically-
May be make sure about this as it says reindex because only you need to rescale
it like in HKL2000. It its wrong I am Sorry in advance.
Date: Wed, 14 Mar 2012 07:43:15 -0500
From: ccp4...@hotmail.com
Subject: Re: [ccp4bb] MTZ file
To: CCP4BB@JISCMAIL.AC.UK
Mahesh,
You should always use output_1.mtz for refinement.
Dont use output_2. mtz for further refinement instead use some ccp4 utilities
to change output_1.mtz (C222) to say output1_mod.mtz (C2221). This will become
your master file for all further refinement. What ever remaining 2.mtz, 3.mtz,
so on you get would only be used in coot and after the modification in coot the
new model will be refined against your output1_mod.mtz (one with correct SG,
now called new master file).
Never use 2,3, 4, mtz files which you get after each round of refinement in
next refinement. So "Am right-now using output_2.mtz, Is it right to use
output_3.mtz ?" - NO
Changing from 1 to 1_mod could be done in HKL2000, at scaling step or maybe
reindex or pointless will do. I am not 100% sure though. May be make sure
about this as it says reindex because only you need to rescale it like in
HKL2000. You could use SFtools and CAD also I guess. These three in all CCP4.
There may be few more in CCP4 on windows, others could give good suggestion
than me.
Hope this helpsRaj
Date: Wed, 14 Mar 2012 16:58:34 +0530
From: mahes1...@gmail.com
Subject: Re: [ccp4bb] MTZ file
To: CCP4BB@JISCMAIL.AC.UK
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
--
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V . MAHESHWARAN
Research Scholar,
Centre of Advanced Study in Crystallography and Biophysics,
University of Madras,
Maraimalai campus,
Guindy,
Madras - 600 025
Mob : 09791767934
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