Re: [ccp4bb] updated mtz file or original one in refmac5
I just checked a recent refmac job and it seems that in the output mtz the Fobs has indeed changed. what's more interesting, the number of missing reflections has changed too (disturbingly, it decreased so that the dataset looks more complete 97.07% to 97.17% in this case). But if the same overall anisotropic B scaling is done every time, there seems to be no harm, right? Ed. On Tue, 2010-05-18 at 05:10 +0100, Frank von Delft wrote: Hi Jay No, don't use the new one: the F's in there have been scaled by the overall anisotropic B-factors. (At least, they used to be, a few years ago.) Definitely go with the old one, every time. The output mtz has the coefficients for the maps, that's all. Cheers phx. On 17/05/2010 18:26, Ian Tickle wrote: Hi Jay I always use the original, I only use the new one for maps deposition of Fcalc etc. But I don't think it does any harm to use the new one, all the info is copied over. HTH. Cheers -- Ian On Mon, May 17, 2010 at 5:25 PM, Jay Panccp4p...@gmail.com wrote: Hello every one, I am just starting to use refmac to do refinement. There is an mtz output file each time. Should I use this one for further refinement or should I use the original mtz file (the one after scaling)? Thanks. Jay -- 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 /
Re: [ccp4bb] updated mtz file or original one in refmac5
The decrease in missing reflections are due to the fact that the output file does not include the missing reflections that are lower resolution than the lowest resolution observed reflection. Thus, this file is no longer uniqueified and then refmac reports a higher completeness since it no longer counts the missing low resolution reflections as missing. In addition, if you are using experimental phase restraints, these data columns are not included in the output. I would recommend always using the same input data file for each round of refinement. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ed Pozharski Sent: Tuesday, May 18, 2010 6:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] updated mtz file or original one in refmac5 I just checked a recent refmac job and it seems that in the output mtz the Fobs has indeed changed. what's more interesting, the number of missing reflections has changed too (disturbingly, it decreased so that the dataset looks more complete 97.07% to 97.17% in this case). But if the same overall anisotropic B scaling is done every time, there seems to be no harm, right? Ed. On Tue, 2010-05-18 at 05:10 +0100, Frank von Delft wrote: Hi Jay No, don't use the new one: the F's in there have been scaled by the overall anisotropic B-factors. (At least, they used to be, a few years ago.) Definitely go with the old one, every time. The output mtz has the coefficients for the maps, that's all. Cheers phx. On 17/05/2010 18:26, Ian Tickle wrote: Hi Jay I always use the original, I only use the new one for maps deposition of Fcalc etc. But I don't think it does any harm to use the new one, all the info is copied over. HTH. Cheers -- Ian On Mon, May 17, 2010 at 5:25 PM, Jay Panccp4p...@gmail.com wrote: Hello every one, I am just starting to use refmac to do refinement. There is an mtz output file each time. Should I use this one for further refinement or should I use the original mtz file (the one after scaling)? Thanks. Jay -- 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 /
Re: [ccp4bb] updated mtz file or original one in refmac5
On Tue, 2010-05-18 at 07:03 -0700, Miller, Mitchell D. wrote: The decrease in missing reflections are due to the fact that the output file does not include the missing reflections that are lower resolution than the lowest resolution observed reflection. Thus, this file is no longer uniqueified and then refmac reports a higher completeness since it no longer counts the missing low resolution reflections as missing. In addition, if you are using experimental phase restraints, these data columns are not included in the output. I would recommend always using the same input data file for each round of refinement. Hmm... The listed resolution limits are the same. Using the original mtz file in every round is of course the best (and in fact with ccp4i it takes an extra effort to do otherwise. At least for me, the Re-run job button fan :)) -- 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] updated mtz file or original one in refmac5
Hello every one, I am just starting to use refmac to do refinement. There is an mtz output file each time. Should I use this one for further refinement or should I use the original mtz file (the one after scaling)? Thanks. Jay
Re: [ccp4bb] updated mtz file or original one in refmac5
Hi Jay I always use the original, I only use the new one for maps deposition of Fcalc etc. But I don't think it does any harm to use the new one, all the info is copied over. HTH. Cheers -- Ian On Mon, May 17, 2010 at 5:25 PM, Jay Pan ccp4p...@gmail.com wrote: Hello every one, I am just starting to use refmac to do refinement. There is an mtz output file each time. Should I use this one for further refinement or should I use the original mtz file (the one after scaling)? Thanks. Jay
Re: [ccp4bb] updated mtz file or original one in refmac5
Hi Jay No, don't use the new one: the F's in there have been scaled by the overall anisotropic B-factors. (At least, they used to be, a few years ago.) Definitely go with the old one, every time. The output mtz has the coefficients for the maps, that's all. Cheers phx. On 17/05/2010 18:26, Ian Tickle wrote: Hi Jay I always use the original, I only use the new one for maps deposition of Fcalc etc. But I don't think it does any harm to use the new one, all the info is copied over. HTH. Cheers -- Ian On Mon, May 17, 2010 at 5:25 PM, Jay Panccp4p...@gmail.com wrote: Hello every one, I am just starting to use refmac to do refinement. There is an mtz output file each time. Should I use this one for further refinement or should I use the original mtz file (the one after scaling)? Thanks. Jay
