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Re: [ccp4bb] GUI problem with SIGMAA |
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CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 20 April 2007Subject: Re: GUI problem with SIGMAA From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU Date: 2007-04-20 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: 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 <-- 20 April 2007 |
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