Re: [ccp4bb] 100% Rmerge in high resolution shell
Usually this means that you have relatively high multiplicity, which give-or-take improves the I/sig(I) by sqrt(m) where m is the multiplicity, but also increases the Rmerge. For any given narrow shell of reflections, Rmerge ~ 0.8 / unmerged(I/sig(I)) merged(I/sig(I)) ~ sqrt(m) * unmerged(I/sig(I)) So it is perfectly possible to have unmerged I/sig(I) of 0.8 which will give you an Rmerge of around 1.0, and have I/sig(I) (merged) around 3, by having multiplciity 14 or so. I suggest that this is the case: if it is much lower than this there is something odd going on. For the merged I/sig(I) Rpim is much more instructive. I'd love it if people reported merged and unmerged I/sig(I), Rmerge, Rmeas, Rpim, CC1/2, ... as each of these tells something different. Best wishes, Graeme Possibly useful papers: http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html http://scripts.iucr.org/cgi-bin/paper?he0191 http://scripts.iucr.org/cgi-bin/paper?he0268 On 19 November 2013 06:43, Shanti Pal Gangwar gangwar...@gmail.com wrote: Dear All Can anyone explain the meaning and relevance of data when the Rmerge is 100% in high resolution shell and I/sig(I) is 3. Thanks -- regards Shanti Pal Gangwar School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.com
Re: [ccp4bb] 100% Rmerge in high resolution shell
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Graeme, On 11/19/2013 09:02 AM, Graeme Winter wrote: [...] For the merged I/sig(I) Rpim is much more instructive. I'd love it if people reported merged and unmerged I/sig(I), Rmerge, Rmeas, Rpim, CC1/2, ... as each of these tells something different. Depending on where you publish the editor will ask you to use their standard layout for the table which was probably last updated in the 1990's given the presence of something as sophisticated as an Rfree... That's my recent experience, which undermined my preference for scientifically sound journals over tabloids. Unfortunately, it's the latter that funding agency like better ... Best, Tim Best wishes, Graeme Possibly useful papers: http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html http://scripts.iucr.org/cgi-bin/paper?he0191 http://scripts.iucr.org/cgi-bin/paper?he0268 On 19 November 2013 06:43, Shanti Pal Gangwar gangwar...@gmail.com wrote: Dear All Can anyone explain the meaning and relevance of data when the Rmerge is 100% in high resolution shell and I/sig(I) is 3. Thanks -- regards Shanti Pal Gangwar School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.com - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSizAgUxlJ7aRr7hoRAtW8AJ9faxDJ6Wz2F5frob8PlOOXne2ZMACfdGxv fA0SSd2GsXKQRqZwg6MHjOk= =fyIi -END PGP SIGNATURE-
Re: [ccp4bb] 100% Rmerge in high resolution shell
I've generally found that adding lines to the standard table works, and they are not removed by editors On 19 Nov 2013, at 09:32, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Graeme, On 11/19/2013 09:02 AM, Graeme Winter wrote: [...] For the merged I/sig(I) Rpim is much more instructive. I'd love it if people reported merged and unmerged I/sig(I), Rmerge, Rmeas, Rpim, CC1/2, ... as each of these tells something different. Depending on where you publish the editor will ask you to use their standard layout for the table which was probably last updated in the 1990's given the presence of something as sophisticated as an Rfree... That's my recent experience, which undermined my preference for scientifically sound journals over tabloids. Unfortunately, it's the latter that funding agency like better ... Best, Tim Best wishes, Graeme Possibly useful papers: http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html http://scripts.iucr.org/cgi-bin/paper?he0191 http://scripts.iucr.org/cgi-bin/paper?he0268 On 19 November 2013 06:43, Shanti Pal Gangwar gangwar...@gmail.com wrote: Dear All Can anyone explain the meaning and relevance of data when the Rmerge is 100% in high resolution shell and I/sig(I) is 3. Thanks -- regards Shanti Pal Gangwar School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.com - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSizAgUxlJ7aRr7hoRAtW8AJ9faxDJ6Wz2F5frob8PlOOXne2ZMACfdGxv fA0SSd2GsXKQRqZwg6MHjOk= =fyIi -END PGP SIGNATURE-
Re: [ccp4bb] 100% Rmerge in high resolution shell
Graeme wrote: ... Rpim is much more instructive. ... as each of these tells something different. I have to ask: Why is Rpim much more instructive? I'm trying to figure this out still. Can one please summarize what are best practices with all these numbers and how each of these tells something different? Another problem that I see is that folks can adjust their sigmas many different ways without knowing they have adjusted their sigmas. And they can be adjusted incorrectly when they are adjusted. BTW, Graeme is correct about lots of multiple low I/sigI observations for each Bragg reflection in a resolution shell will lead to 100% (or higher) Rmerge with I/sigI of 3. This assumes no systematic errors and only randomly distributed random errors (a rare if not impossible situation, I would think). I will defer to others about what the relevance of that is. Thanks for any insights, Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Graeme Winter [graeme.win...@gmail.com] Sent: Tuesday, November 19, 2013 2:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 100% Rmerge in high resolution shell Usually this means that you have relatively high multiplicity, which give-or-take improves the I/sig(I) by sqrt(m) where m is the multiplicity, but also increases the Rmerge. For any given narrow shell of reflections, Rmerge ~ 0.8 / unmerged(I/sig(I)) merged(I/sig(I)) ~ sqrt(m) * unmerged(I/sig(I)) So it is perfectly possible to have unmerged I/sig(I) of 0.8 which will give you an Rmerge of around 1.0, and have I/sig(I) (merged) around 3, by having multiplciity 14 or so. I suggest that this is the case: if it is much lower than this there is something odd going on. For the merged I/sig(I) Rpim is much more instructive. I'd love it if people reported merged and unmerged I/sig(I), Rmerge, Rmeas, Rpim, CC1/2, ... as each of these tells something different. Best wishes, Graeme Possibly useful papers: http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html http://scripts.iucr.org/cgi-bin/paper?he0191 http://scripts.iucr.org/cgi-bin/paper?he0268 On 19 November 2013 06:43, Shanti Pal Gangwar gangwar...@gmail.commailto:gangwar...@gmail.com wrote: Dear All Can anyone explain the meaning and relevance of data when the Rmerge is 100% in high resolution shell and I/sig(I) is 3. Thanks -- regards Shanti Pal Gangwar School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.commailto:email%3agangwar...@gmail.com
Re: [ccp4bb] 100% Rmerge in high resolution shell
: ... Rpim is much more instructive. ... as each of these tells something different. I have to ask: Why is Rpim much more instructive? I'm trying to figure this out still. Can one please summarize what are best practices with all these numbers and how each of these tells something different? Another problem that I see is that folks can adjust their sigmas many different ways without knowing they have adjusted their sigmas. And they can be adjusted incorrectly when they are adjusted. BTW, Graeme is correct about lots of multiple low I/sigI observations for each Bragg reflection in a resolution shell will lead to 100% (or higher) Rmerge with I/sigI of 3. This assumes no systematic errors and only randomly distributed random errors (a rare if not impossible situation, I would think). I will defer to others about what the relevance of that is. Thanks for any insights, Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Graeme Winter [graeme.win...@gmail.com] Sent: Tuesday, November 19, 2013 2:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 100% Rmerge in high resolution shell Usually this means that you have relatively high multiplicity, which give-or-take improves the I/sig(I) by sqrt(m) where m is the multiplicity, but also increases the Rmerge. For any given narrow shell of reflections, Rmerge ~ 0.8 / unmerged(I/sig(I)) merged(I/sig(I)) ~ sqrt(m) * unmerged(I/sig(I)) So it is perfectly possible to have unmerged I/sig(I) of 0.8 which will give you an Rmerge of around 1.0, and have I/sig(I) (merged) around 3, by having multiplciity 14 or so. I suggest that this is the case: if it is much lower than this there is something odd going on. For the merged I/sig(I) Rpim is much more instructive. I'd love it if people reported merged and unmerged I/sig(I), Rmerge, Rmeas, Rpim, CC1/2, ... as each of these tells something different. Best wishes, Graeme Possibly useful papers: http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html http://scripts.iucr.org/cgi-bin/paper?he0191 http://scripts.iucr.org/cgi-bin/paper?he0268 On 19 November 2013 06:43, Shanti Pal Gangwar gangwar...@gmail.commailto:gangwar...@gmail.com wrote: Dear All Can anyone explain the meaning and relevance of data when the Rmerge is 100% in high resolution shell and I/sig(I) is 3. Thanks -- regards Shanti Pal Gangwar School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.commailto:email%3agangwar...@gmail.com -- 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] 100% Rmerge in high resolution shell
Dear All Can anyone explain the meaning and relevance of data when the Rmerge is 100% in high resolution shell and I/sig(I) is 3. Thanks -- regards Shanti Pal Gangwar School of Life Sciences Jawaharlal Nehru University New Delhi-110067 India Email:gangwar...@gmail.com
