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I don't understand all of this,but the MTZ files does contain the cells in
the Batch headers, and Scala uses these as the master cell dimensions. At
present there is no easy way to change these :-(
However, if you are merging these files from the same crystal, you are
assuming the unit cell is constant, and the programs have no easy way to
determine which is best (which is why Scala takes an average).
If you have a better idea of the cell, you can change it later with eg CAD
Determining accurate cell dimensions is not trivial, and will be less
accurate at low resolution (and also wrong if your wavelength is wrong)
Phil
Hi all,
We have found a puzzle about cell dimensions. Not really a problem, just
something a bit confusing. This is our scenario:
1. We collected data in two passes (high and low resolution)
2. The high and low resolution passes were integrated with mosflm,
producing two mtz files. The cell dimensions as output by mosflm and
read from these mtz files are respectively:
HR: 42.6287 191.4204 71.9418 90.0000 90.0000 90.0000
LR: 42.6423 191.1283 71.9388 90.0000 90.0000 90.0000
(OK, we could have forced the LR pass to have the same cell, but somehow
it happened to be refined)
3. We put them together using sortmtz. The header of the resulting mtz
file says:
8<-------------------------------------------------------------->8
* Title:
.
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 2
* Dataset ID, project/crystal/dataset names, cell dimensions,
wavelength:
1 Mer
p67B1
natHR180
42.6423 191.1283 71.9388 90.0000 90.0000 90.0000
0.93400
2 Mer
p67B1
natLR180
42.6423 191.1283 71.9388 90.0000 90.0000 90.0000
0.93400
* Number of Columns = 18
* Number of Reflections = 280753
* Missing value set to NaN in input mtz file
* Number of Batches = 360
* HISTORY for current MTZ file :
From SORTMTZ 18/ 9/2006 11:01:19 using keys: H K L M/ISYM BATCH
From MOSFLM run on 18/ 9/06
* Column Labels :
H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH
LP MPART FLAG BGPKRATIOS
* Column Types :
H H H Y B J Q J Q R R R R R R I I R
* Associated datasets :
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions
above)
42.6423 191.1283 71.9388 90.0000 90.0000 90.0000
* Resolution Range :
0.00011 0.25071 ( 95.783 - 1.997 A )
- ---------------------------------------------------------------->8
So, first problem/feature/bug: sortmtz assigns to the first dataset
(HR) the cell dimensions of the second one (LR).
4. We then scaled together with scala these data, producing a new
combined dataset. When scala reads the mtz from the previous step it
outputs these warnings:
8<----------------------------------------------------------------
WARNING: output dataset Mer/p67B1/native180 contains input datasets
with different Project Names
WARNING: output dataset Mer/p67B1/native180 contains input datasets
with different Crystal Names
===== Dataset: Mer/p67B1/native180
Run(s): 1 2
* Wavelength and cell extracted from Batch headers, with rms variation:
* Wavelength: 0.934000 Cell: 42.636 191.274 71.940 90.000
90.000 90.000
* rms 0.000000 rms 0.000 0.139 0.000 0.000
0.000 0.000
Wavelength: 0.934000 Cell: 42.636 191.274 71.940 90.000
90.000 90.000
- ---------------------------------------------------------------->8
I don't understand the warnings: it is precisely the Project and
Crystal names which are identical, only the output dataset (native180)
being different from the input ones (natHR180 and natLR180). I also
notice that the cell shown here is an average from the HR and LR
datasets. This cell is also the one obtained in the output mtz from
scala. Thus, I deduce that the HR cell is somehow present in the mtz
that comes from sortmtz, though I cannot see it in its header.
All this may be good and well, but I find it a bit confusing, and
that's why I report it.
Cheers,
Miguel
- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [EMAIL PROTECTED]
www: http://www.ysbl.york.ac.uk/~mol/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en liberté
Dans les jardins mal fréquentés!
Georges Brassens
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