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Re: [ccp4bb] How to run SIGMAA twice in a row? (fwd) |
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CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 19 April 2007Subject: Re: How to run SIGMAA twice in a row? (fwd) From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU Date: 2007-04-19 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: hli@uci.edu >> -------------------------------------------------- >> >> > -- ------------------------------------------------- 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: hli@uci.edu -------------------------------------------------- CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 19 April 2007 |
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