The preferred general route into CCP4 for unmerged data for scaling and merging
(if that is what you want to do) is through Pointless into Scala (or in future
Aimless as a Scala replacement, or the future merged Pointless/Aimless
(nameless)).
At present Pointless will accept data from Mosflm,
Hi Madhu,
You don't need to use scala, d*trek can do the job as well. The easiest thing
to do is to continue with d*trek to scale and merge your data and then input
this scaled and merged file into Dtrek2mtz.
Eric
Eric T. Larson, PhD
Biomolecular Structure
HI,
I indexed and integrated data from RAXIS(Rigaku) detector on
'Crystalclear'. It gave me a .cif file as output.I am not able to read
this file in ccp4 to carry out rest of the analysis in ccp4. I want to
know how to convert this cif file to MTZ.
Thanks
Madhu
Easiest way:
CCP4i
Reflection Data Utilities
Convert to MTZ
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Madhu
shankar Madhu shankar
Sent: Thursday, June 23, 2011 5:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Convert .cif to mtz
HI
Hi Madhu,
D*trek is what you processed your data with. In the ccp4i gui, select the program Dtrek2mtz and
then in the field that says convert scaled data output from ... , select d*trek from
the pull down menu. Go to http://www.ccp4.ac.uk/html/dtrek2mtz.html for more information.
good luck,
Madhu,
I just noticed that your message said you indexed and integrated your data.
Did you scale it with d*trek too (that needs to be done before using Dtrek2mtz) or are
you looking to use the integrated d*trek reflections for subsequent scaling in ccp4 with
scala?
Eric
On Thu, 23 Jun
HI Eric,
I havent yet done the scala ,i have just indexed and
integrated the data in d*trek. I tried converting the .cif in
Dtrek2mtz but thats failed.
Thanks Madhu
The underlying program cif2mtz will convert everything it can recognise,
i.e. it will convert intensities or amplitudes or both, depending on
what is there.
But what is actually in a PDB cif structure factor file varies greatly.
For a start, there's a high chance there are no phases, so no map
I'm looking for a convenient way of converting a .cif structure factor file
(from PDB) to a map-file (e.g. .mtz) to open with COOT for example..?
Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a bunch of
errors when opening with coot..
doesn't coot have an 'import from EDS'
It has just worked for me?
convert to mtz
file type mmCIF
then I had to put in my own cell and spacegroup.
And I will have to calculate phases before I can use coot with it..
Eleanor
Eleanor
It looks like this..
#
_audit.revision_id1_0
_audit.creation_date 2005-03-22
In recent coots, (This is 0.4.1, kendall, on a mac or linux) you no
longer need to calculate fcalc and phases. If you choose auto open
mtz and have at least one pdb file open, coot will ask you which pdb
file to use to calculate fcalc and phases. (I guess it runs refmac
then) and, voila,
The GUI actually is a quite convenient way. In my experience, however, the
GUI or the program called by the GUI does not check whether the cif
contains intensities or amplitudes. So you can use the GUI, look at the
script it generates and adjust it according to the header in your cif.
Tim
--
Dear all,
I'm looking for a convenient way of converting a .cif structure
factor file (from PDB) to a map-file (e.g. .mtz) to open with COOT
for example..?
Already tried ccp4i with 'Convert to/modify/extend MTZ', but got a
bunch of errors when opening with coot..
Many thanks
Kristof
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