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Hi Daniel,
Try this
sftools
read lowres.mtz
read highres.mtz column FreeR_flag (or the name you use for Rfree)
write lowresFreeR.mtz
exit
This reads your low resolution data set, adds and mergens the Rfree
column from the high resolution and write them all out to the new mtz.
If you want you can remove the high resolution Rfree entries by
select resol > 2.218 (assuming 2.218 is your max res)
To find out max resolution type
checkhkl
If the original rfree set had a random selection of 5% of reflections
than it should again be approximately 5% in the new dataset. If you want
to confirm this then you must count the number of zeroes in the column
and compare it to the total number of reflections. If you use 1 for the
working set flag then the checkhkl table should tell you that the
average FreeR_flag column value is about 0.95 (5% zeroes & 95% ones).
You can also use
plot col FreeR_flag versus resolution
and you get the percent as function of resolution. If your working set
reflections have different values than just using 1, then you must set
them to one before looking at the stats. You do that by typing
select col FreeR_flag > 0
calc col FreeR_flag = 1
select all
plot col FreeR_flag versus resolution
Bart
PS: for the perfectionist, you should add a
select col Fp present
before looking at the stats to ensure they are based only on the
reflections for which an Fobs observation exists (assuming your Fobs
column name is fp.
Daniel Gurmu wrote:
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Dear All,
I am trying to copy an existing Rfree set from a high resolution (1.9 A)
to a low resolution dataset (2.8 A). I followed the instructions from
the ccp4 documentation (under FreeR information). Running cad, I limited
the resolution for the input mtz to 2.8, so as not to copy Rfree column
values for the higher resolution reflections.
How can I make sure that the Rfree set is 5% for the low resolution
dataset, after copying the Rfree set. How can I obtain information about
the size of the Rfree in the resulting mtz file (mtzdump does not
provide this information)?
Is there a program to do that? I have tried DATAMAN (from the Uppsala
suite) but failed to load the mtz file from ccp4:
DATAMAN > re m1 xtal_5_1__001_SCALA_CAD_2.mtz
File type ? (*) ELEANOR
File : (xtal_5_1__001_SCALA_CAD_2.mtz)
Type : (ELEANOR)
Format : (*)
ERROR --- While reading reflection file
Nr of reflections read : ( 0)
Also, I ran uniqueify with the -f option after running cad. This seems
reasonable if the copied Rfree set does not make up more than 5% in the
final (low-resolution) dataset.
I am concerned about the situation if the copied RFree set exceeds 5% in
the final (low-resolution) dataset and about an even distribution of the
Rfree reflections in the resolution bins. I could only find an option to
remove reflections and change the bin distribution in the DATAMAN
manual. Is there an alternative way in ccp4?
What is the optimal way to do this?
Regards,
Daniel
--
==============================================================================
Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
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