Hi Eleanor,
Thanks for doing the test. I did the same thing through run & view com
option as Chris Rife suggested. SIGMMA did wonderful job once I was able
to provide the second run with the correct FOM from the first round of
MAD phase combination. The density quality (after SOLOMON) calculated with
correct FOM is much better than the one with the FOMmad (the one I could
only select through the GUI). With the much improved density we were able
to fit in most of the side chains.
Thanks again for everyone who offered help.
Huiying
On Fri, 20 Apr 2007, Eleanor Dodson wrote:
I cant find any test data - will have to create it to test properly..
Eleanor
Have done so.. things are exactly asd you describe them
I ran the first job with 2 sets oF PHI and HL coeffs
Output PHCMBtest1 WCMBtest1 HLACMBtest1 etc
Then tried second and as you said there was no FOM allowed for the input
"experimental" phase PHCMBtest1
It runs OK if I use the option run and view com file and insert the extra
info into the LABI line
LABI FP= PHIBP=PHCMBtest1 etc and then I add WP=WCMBtest1
But that shouldnt be necessary as you say..
The only peculiarity I can see in the first SigmaA output is that the
combined phases are in data set 0, but changing that doesnt help.
Any ideas GUI experts???
Eleanor
Huiying Li wrote:
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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