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Re: [ccp4bb] Question about freeR tag |
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CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 23 January 2008Subject: Re: Question about freeR tag From: Edwin Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU Date: 2008-01-23 description says when describing the keyword SEED: By default, for a given job on a given machine, the random number generator produces the same list of "random" free-R flags each time the job is run. Since you would generally only produce one list of free-R flags for each project, this is not usually a problem. However, if you specify the keyword SEED, then the random number generator is seeded with the current time, and will produce a different list of free-R flags each time the job is run. So what you see is normal. Zheng Zhou wrote: > Sorry that I didn't explain the situation clearly. I used only one > output.sca file from HLK2000. I ran the scalepack2mtz (in CCP4i, data > reduction, import merged data) several times, on both linux Fedora and > window XP, the same computer though. > > For the next step refinement, I mean add H2O, ion, ligands, double > check certain sidechains.... In those refmac runs, I always use the > same mtz file, which I generated from the beginning. I am as surprised > as you are the Rfree flags are identical from those different "first" > runs. > > Thanks > > On Jan 23, 2008 9:50 AM, Zheng Zhou > > > Hi, All > > Could any tell me how CCP4 handle free R flag? I know It is > important to select the same FreeR reflections if I move to next > step of refinement. But everytime I start from fresh, the freeR > Flag remains unchanged. The Rwork and Rfree of my models are fine > ( 20.7% and 22.9%). I thought Rfree was randomly generated. I > asked more experienced people in the lab and neighbor labs, and > didn't get a straight answer. Did I do something wrong? > > Thanks and sorry to bother others. > > Zheng (Joe) > > I cant understand this. > Do you mean you have multiple data sets and they all generate the same > FreeRs? If you have EXACTLY the same reflection list, and generate FreeR > flags on the same machine I guess they would be the same.. but it would > be surprising > > Or if you are using the same file which already has FreeR flags then > they wont change of course - the default is always to use the > reflections flagged with FreeR = 0. (Thats as it should be..) > > By the by - your agreement between R and FreeR seems unusually low > unless you have very high resolution data or a great deal of > non-crystallographic symmetry. > Eleanor > > Zheng - I am not sure what you are doing, but as long as you work > with one dataset only, you generate the free reflections at the very > beginning when you import your data into CCP4. Then use the resulting > mtz file for all following refinement steps. There are situations > where one will have to deviate from this scheme, but those are rare. > If you feel you have such a case, then tell us more about it. Hope > that helps. Best - MM > > Joe, > > > can you explain a bit clearer your problem? what do you mean the > 'next step of refinement'? are you just doing another round of > refinement? what program are you using, REFMAC5? also, R/Rfree of > 20.7/22.9 is pretty good, depending on resolution. > > yes, you are right, Rfree flags are generated randomly and can be > anywhere from 5-10% of your reflections (your choice). then, once the > Rfree flagged reflections are selected, they will not change (nor be > refined) throughout the rest of your structure determination. they > should have their own column in your *.mtz file called RfreeFlag or > something like this (in CCP4 that is). other programs handle this > relatively the same, but may use various naming conventions. one > caveat is that CCP4 flags reflections using 0 by default (meaning 5% > of your reflections are flagged with 0 and are the Rfree set). Other > programs such as CNS and PHENIX use 1 by default, so be careful when > switching back and forth. You can tell either program which to use > for Rfree set, but needs to be set, since it is not default. > > again, not exactly sure what the problem is, but i hope some of this > helps. feel free to email with further questions if needed. best of > luck! > > > > cheers, > nick > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse / CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 23 January 2008 |
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