Thank Eleanor and others for making suggestions. We have tested SIGMAA in
CCP4i(1.4.4.1) again carefully. In the first run, we used "combine two sets of
MIR phases" mode to combine 2 sets of MAD phases, and output column labels
changed to PHCMBtest and WCMBtest. The second run was in "combine isomorphous
phase with partial structure" mode. We had no problem assigning other column
labels such as FP, PHIBP, ... because the pull-down menu of each label includes
"list all labels" option. But FOM pull-down menu had no "list all labels"
option, we could not select the label WCMBtest generated from the previous run.
It seems to me there is a bug in the GUI that limits the option in FOM
pull-down menu. It only occurs in the "combine isomorphous phase with partial
structure" running mode of SIGMAA. This is the run we really wanted to combine
the model phases with the MAD phases before going through further density
modifications with SOLOMON or DM.
Regards,
Huiying
On Thu, 19 Apr 2007, Eleanor Dodson wrote:
Sorry about that
It is ages since I have used SIGMAA
The MAD recombnation gives you PHCMB WCMB HLAC HLBC etc
In that run I would make sure I renamed PHCMB WCMB PHCMBmadsWCMBmads or
something
You might have to use the option Run and view com file, then edit in a line:
LABOUT PHCMB=PHCMBmads WCMB= etc
Then I think you may be able to do what you want - I suspect the poor program
is getting lost between what is a default output label, and something already
in the header.
Can you try that?
Or you use the Clipper utility to combine phases.. it is more mindless but
you do have to convert your PHIC FOM to HLA HLB (HLC HLD ==0) using another
clipper utility first
Eleanor
Huiying Li wrote:
My previous posting did not get answer, it might be a bit confusing. My
questions is if I want to conbine phases from three different sources, 2 MAD
data sets and a partial model, can I run SIGMAA twice? Combining MAD phases
first, and then add in the model phases to the pre-combined MAD phases. When
I run SIGMAA the second time CCP4i GUI allows me to choose labels PHCMB,
HLAC, HLBC, HLCC, HLDC, but doesn't let me use WCMB as the input FOM. Is
this a bug in the GUI or SIGMAA simply does not allow to use WCMB as an
input FOM?
Thanks in advance.
Huiying
-------------------------------------------------
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
email: [EMAIL PROTECTED]
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Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
email: [EMAIL PROTECTED]
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