Re: [ccp4bb] Drawing reaction mechanism
Hi, this one is free: http://www.acdlabs.com/resources/freeware/chemsketch/ Cheers, Daniel -- On Fri, Jun 1, 2012 12:01 AM ART Appu kumar wrote: Dear ccp4 user, Sorry for offset question, Anyone please tell me the name of programme which can be used to draw enzyme reaction mechanism ( like Sn1 and Sn2). Your kind help will be much appreciated Thank you Appu
Re: [ccp4bb] Calculation of volume/size of cavity
You could use Laskowski's surfnet, http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html HTH, Daniel -- On Thu, May 31, 2012 3:59 PM ART Allan Pang wrote: A list that you might want to check if it is useful for you. http://www.caver.cz/index.php?sid=133 Enjoy. Allan Quoting Zhou, Tongqing (NIH/VRC) [E] tz...@mail.nih.gov: Dear All, I am looking for a way to calculate the size of a protein cavity which is occupied by a loop from a ligand protein. The goal is to see what's the maximum length of peptide allowed in this cavity. Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ** --Allan Pang PhD Student G35 Joseph Priestley Building Queen Mary University of London London E1 4NS Phone number: 02078828480 Twitter: @xerophytes
Re: [ccp4bb] Drawing reaction mechanism
Hi Appu, I use ChemDoodle ( http://www.chemdoodle.com ) which works quite well, but unfortunately is not free. You can try the trial version though. Robbert On Fri, Jun 1, 2012 at 4:01 AM, Appu kumar appu.kum...@gmail.com wrote: Dear ccp4 user, Sorry for offset question, Anyone please tell me the name of programme which can be used to draw enzyme reaction mechanism ( like Sn1 and Sn2). Your kind help will be much appreciated Thank you Appu
Re: [ccp4bb] Death of Rmerge
On 1 June 2012 03:22, Edward A. Berry ber...@upstate.edu wrote:
Leo will probably answer better than I can, but I would say I/SigI counts
only
the present reflection, so eliminating noise by anisotropic truncation
should
improve it, raising the average I/SigI in the last shell.
We always include unmeasured reflections with I/sigma(I) = 0 in the
calculation of the mean I/sigma(I) (i.e. we divide the sum of
I/sigma(I) for measureds by the predicted total no of reflections incl
unmeasureds), since for unmeasureds I is (almost) completely unknown
and therefore sigma(I) is effectively infinite (or at least finite but
large since you do have some idea of what range I must fall in). A
shell with I/sigma(I) = 2 and 50% completeness clearly doesn't carry
the same information content as one with the same I/sigma(I) and
100% complete; therefore IMO it's very misleading to quote
I/sigma(I) including only the measured reflections. This also means
we can use a single cut-off criterion (we use mean I/sigma(I) 1),
and we don't need another arbitrary cut-off criterion for
completeness. As many others seem to be doing now, we don't use
Rmerge, Rpim etc as criteria to estimate resolution, they're just too
unreliable - Rmerge is indeed dead and buried!
Actually a mean value of I/sigma(I) of 2 is highly statistically
significant, i.e. very unlikely to have arisen by chance variations,
and the significance threshold for the mean must be much closer to 1
than to 2. Taking an average always increases the statistical
significance, therefore it's not valid to compare an _average_ value
of I/sigma(I) = 2 with a _single_ value of I/sigma(I) = 3 (taking 3
sigma as the threshold of statistical significance of an individual
measurement): that's a case of comparing apples with pears. In
other words in the outer shell you would need a lot of highly
significant individual values 3 to attain an overall average of 2
since the majority of individual values will be 1.
F/sigF is expected to be better than I/sigI because dx^2 = 2Xdx,
dx^2/x^2 = 2dx/x, dI/I = 2* dF/F (or approaches that in the limit . . .)
That depends on what you mean by 'better': every metric must be
compared with a criterion appropriate to that metric. So if we are
comparing I/sigma(I) with a criterion value = 3, then we must compare
F/sigma(F) with criterion value = 6 ('in the limit' of zero I), in
which case the comparison is no 'better' (in terms of information
content) with I than with F: they are entirely equivalent. It's
meaningless to compare F/sigma(F) with the criterion value appropriate
to I/sigma(I): again that's comparing apples and pears!
Cheers
-- Ian
Re: [ccp4bb] Death of Rmerge
Please excuse my ignorance, but I cannot understand why Rmerge is unreliable
for estimation of the resolution?
I mean, from a theoretical point of view, 1/sigma is indeed a better
criterion, but it is not obvious from a practical point of view.
1/sigma depends on a method for sigma estimation, and so same data processed
by different programs may have different 1/sigma. Moreover, HKL2000 allows
users to adjust sigmas manually. Rmerge estimates sigmas from differences
between measurements of same structural factor, and hence is independent of our
preferences. But, it also has a very important ability to validate consistency
of the merged data. If my crystal changed during the data collection, or
something went wrong with the diffractometer, Rmerge will show it immediately,
but 1/sigma will not.
So, please explain why should we stop using Rmerge as a criterion of data
resolution?
Alex
Sanford-Burnham Medical Research Institute
10901 North Torrey Pines Road
La Jolla, California 92037
On Jun 1, 2012, at 5:07 AM, Ian Tickle wrote:
On 1 June 2012 03:22, Edward A. Berry ber...@upstate.edu wrote:
Leo will probably answer better than I can, but I would say I/SigI counts
only
the present reflection, so eliminating noise by anisotropic truncation
should
improve it, raising the average I/SigI in the last shell.
We always include unmeasured reflections with I/sigma(I) = 0 in the
calculation of the mean I/sigma(I) (i.e. we divide the sum of
I/sigma(I) for measureds by the predicted total no of reflections incl
unmeasureds), since for unmeasureds I is (almost) completely unknown
and therefore sigma(I) is effectively infinite (or at least finite but
large since you do have some idea of what range I must fall in). A
shell with I/sigma(I) = 2 and 50% completeness clearly doesn't carry
the same information content as one with the same I/sigma(I) and
100% complete; therefore IMO it's very misleading to quote
I/sigma(I) including only the measured reflections. This also means
we can use a single cut-off criterion (we use mean I/sigma(I) 1),
and we don't need another arbitrary cut-off criterion for
completeness. As many others seem to be doing now, we don't use
Rmerge, Rpim etc as criteria to estimate resolution, they're just too
unreliable - Rmerge is indeed dead and buried!
Actually a mean value of I/sigma(I) of 2 is highly statistically
significant, i.e. very unlikely to have arisen by chance variations,
and the significance threshold for the mean must be much closer to 1
than to 2. Taking an average always increases the statistical
significance, therefore it's not valid to compare an _average_ value
of I/sigma(I) = 2 with a _single_ value of I/sigma(I) = 3 (taking 3
sigma as the threshold of statistical significance of an individual
measurement): that's a case of comparing apples with pears. In
other words in the outer shell you would need a lot of highly
significant individual values 3 to attain an overall average of 2
since the majority of individual values will be 1.
F/sigF is expected to be better than I/sigI because dx^2 = 2Xdx,
dx^2/x^2 = 2dx/x, dI/I = 2* dF/F (or approaches that in the limit . . .)
That depends on what you mean by 'better': every metric must be
compared with a criterion appropriate to that metric. So if we are
comparing I/sigma(I) with a criterion value = 3, then we must compare
F/sigma(F) with criterion value = 6 ('in the limit' of zero I), in
which case the comparison is no 'better' (in terms of information
content) with I than with F: they are entirely equivalent. It's
meaningless to compare F/sigma(F) with the criterion value appropriate
to I/sigma(I): again that's comparing apples and pears!
Cheers
-- Ian
Re: [ccp4bb] Death of Rmerge
As the K D paper points out, as the signal/noise declines at higher resolution, Rmerge goes up to infinity, so there is no sensible way to set a limiting value to determine resolution. That is not to say that Rmerge has no use: as you say it's a reasonably good metric to plot against image number to detect a problem. It just not a suitable metric for deciding resolution I/sigI is pretty good for this, even though the sigma estimates are not very reliable. CC1/2 is probably better since it is independent of sigmas and has defined values from 1.0 down to 0.0 as signal/noise decreases. But we should be careful of any dogma which says what data we should discard, and what the cutoff limits should be: I/sigI 3,2, or 1? CC1/2 0.2, 0.3, 0.5 ...? Usually it does not make a huge difference, but why discard useful data? Provided the data are properly weighted in refinement by weights incorporating observed sigmas (true in Refmac, not true in phenix.refine at present I believe), adding extra weak data should do no harm, at least out to some point. Program algorithms are improving in their treatment of weak data, but are by no means perfect. One problem as discussed earlier in this thread is that we have got used to the idea that nominal resolution is a single number indicating the quality of a structure, but this has never been true, irrespective of the cutoff method. Apart from the considerable problem of anisotropy, we all need to note the wisdom of Ethan Merritt We should also encourage people not to confuse the quality of the data with the quality of the model. Phil On 1 Jun 2012, at 18:59, aaleshin wrote: Please excuse my ignorance, but I cannot understand why Rmerge is unreliable for estimation of the resolution? I mean, from a theoretical point of view, 1/sigma is indeed a better criterion, but it is not obvious from a practical point of view. 1/sigma depends on a method for sigma estimation, and so same data processed by different programs may have different 1/sigma. Moreover, HKL2000 allows users to adjust sigmas manually. Rmerge estimates sigmas from differences between measurements of same structural factor, and hence is independent of our preferences. But, it also has a very important ability to validate consistency of the merged data. If my crystal changed during the data collection, or something went wrong with the diffractometer, Rmerge will show it immediately, but 1/sigma will not. So, please explain why should we stop using Rmerge as a criterion of data resolution? Alex Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Road La Jolla, California 92037 On Jun 1, 2012, at 5:07 AM, Ian Tickle wrote: On 1 June 2012 03:22, Edward A. Berry ber...@upstate.edu wrote: Leo will probably answer better than I can, but I would say I/SigI counts only the present reflection, so eliminating noise by anisotropic truncation should improve it, raising the average I/SigI in the last shell. We always include unmeasured reflections with I/sigma(I) = 0 in the calculation of the mean I/sigma(I) (i.e. we divide the sum of I/sigma(I) for measureds by the predicted total no of reflections incl unmeasureds), since for unmeasureds I is (almost) completely unknown and therefore sigma(I) is effectively infinite (or at least finite but large since you do have some idea of what range I must fall in). A shell with I/sigma(I) = 2 and 50% completeness clearly doesn't carry the same information content as one with the same I/sigma(I) and 100% complete; therefore IMO it's very misleading to quote I/sigma(I) including only the measured reflections. This also means we can use a single cut-off criterion (we use mean I/sigma(I) 1), and we don't need another arbitrary cut-off criterion for completeness. As many others seem to be doing now, we don't use Rmerge, Rpim etc as criteria to estimate resolution, they're just too unreliable - Rmerge is indeed dead and buried! Actually a mean value of I/sigma(I) of 2 is highly statistically significant, i.e. very unlikely to have arisen by chance variations, and the significance threshold for the mean must be much closer to 1 than to 2. Taking an average always increases the statistical significance, therefore it's not valid to compare an _average_ value of I/sigma(I) = 2 with a _single_ value of I/sigma(I) = 3 (taking 3 sigma as the threshold of statistical significance of an individual measurement): that's a case of comparing apples with pears. In other words in the outer shell you would need a lot of highly significant individual values 3 to attain an overall average of 2 since the majority of individual values will be 1. F/sigF is expected to be better than I/sigI because dx^2 = 2Xdx, dx^2/x^2 = 2dx/x, dI/I = 2* dF/F (or approaches that in the limit . . .) That depends on what you mean by 'better': every metric must be compared with a criterion
Re: [ccp4bb] Death of Rmerge
http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html
http://scripts.iucr.org/cgi-bin/paper?S0021889800018227
Just collect 360 sweep instead of 180 on a non-decaying crystal and see
Rmerge go up due to increase in multiplicity (and enough with redundancy
term - the extra data is not really *redundant*). Is your resolution
worse or better?
This has been argued over before. Rmerge has some value in comparing
two datasets collected in perfectly identical conditions to see which
crystal is better and it may predict to some extent what R-values you
might expect. Otherwise, it's unreliable.
Given that it's been 15 years since this was pointed out in no less than
Nature group magazine, and we still hear that Rmerge should decide
resolution cutoff, chances are increasingly slim that I will personally
see the dethroning of that other major oppressor, R-value.
On Fri, 2012-06-01 at 10:59 -0700, aaleshin wrote:
Please excuse my ignorance, but I cannot understand why Rmerge is unreliable
for estimation of the resolution?
I mean, from a theoretical point of view, 1/sigma is indeed a better
criterion, but it is not obvious from a practical point of view.
1/sigma depends on a method for sigma estimation, and so same data
processed by different programs may have different 1/sigma. Moreover,
HKL2000 allows users to adjust sigmas manually. Rmerge estimates sigmas from
differences between measurements of same structural factor, and hence is
independent of our preferences. But, it also has a very important ability to
validate consistency of the merged data. If my crystal changed during the
data collection, or something went wrong with the diffractometer, Rmerge will
show it immediately, but 1/sigma will not.
So, please explain why should we stop using Rmerge as a criterion of data
resolution?
Alex
Sanford-Burnham Medical Research Institute
10901 North Torrey Pines Road
La Jolla, California 92037
On Jun 1, 2012, at 5:07 AM, Ian Tickle wrote:
On 1 June 2012 03:22, Edward A. Berry ber...@upstate.edu wrote:
Leo will probably answer better than I can, but I would say I/SigI counts
only
the present reflection, so eliminating noise by anisotropic truncation
should
improve it, raising the average I/SigI in the last shell.
We always include unmeasured reflections with I/sigma(I) = 0 in the
calculation of the mean I/sigma(I) (i.e. we divide the sum of
I/sigma(I) for measureds by the predicted total no of reflections incl
unmeasureds), since for unmeasureds I is (almost) completely unknown
and therefore sigma(I) is effectively infinite (or at least finite but
large since you do have some idea of what range I must fall in). A
shell with I/sigma(I) = 2 and 50% completeness clearly doesn't carry
the same information content as one with the same I/sigma(I) and
100% complete; therefore IMO it's very misleading to quote
I/sigma(I) including only the measured reflections. This also means
we can use a single cut-off criterion (we use mean I/sigma(I) 1),
and we don't need another arbitrary cut-off criterion for
completeness. As many others seem to be doing now, we don't use
Rmerge, Rpim etc as criteria to estimate resolution, they're just too
unreliable - Rmerge is indeed dead and buried!
Actually a mean value of I/sigma(I) of 2 is highly statistically
significant, i.e. very unlikely to have arisen by chance variations,
and the significance threshold for the mean must be much closer to 1
than to 2. Taking an average always increases the statistical
significance, therefore it's not valid to compare an _average_ value
of I/sigma(I) = 2 with a _single_ value of I/sigma(I) = 3 (taking 3
sigma as the threshold of statistical significance of an individual
measurement): that's a case of comparing apples with pears. In
other words in the outer shell you would need a lot of highly
significant individual values 3 to attain an overall average of 2
since the majority of individual values will be 1.
F/sigF is expected to be better than I/sigI because dx^2 = 2Xdx,
dx^2/x^2 = 2dx/x, dI/I = 2* dF/F (or approaches that in the limit . . .)
That depends on what you mean by 'better': every metric must be
compared with a criterion appropriate to that metric. So if we are
comparing I/sigma(I) with a criterion value = 3, then we must compare
F/sigma(F) with criterion value = 6 ('in the limit' of zero I), in
which case the comparison is no 'better' (in terms of information
content) with I than with F: they are entirely equivalent. It's
meaningless to compare F/sigma(F) with the criterion value appropriate
to I/sigma(I): again that's comparing apples and pears!
Cheers
-- Ian
--
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
Re: [ccp4bb] Death of Rmerge
I don't think any data should be discarded, and I think that although we are not there yet, refinement should work directly with the images, iterating back and forth through all the various levels of data processing. As I think was pointed out by Wang, even an intensity of 0 provides information placing limits on the possible true values of that reflection. It seems that the main reason data were discarded historically was because of the limitations of (under)grad students going through multiple layers of films, evaluating intensities for each spot, or other similar processing limits, most of which are not really applicable today. A whole iterated refinement protocol now takes, what, 15 minutes? Jacob On Fri, Jun 1, 2012 at 1:29 PM, Ed Pozharski epozh...@umaryland.edu wrote: http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html http://scripts.iucr.org/cgi-bin/paper?S0021889800018227 Just collect 360 sweep instead of 180 on a non-decaying crystal and see Rmerge go up due to increase in multiplicity (and enough with redundancy term - the extra data is not really *redundant*). Is your resolution worse or better? This has been argued over before. Rmerge has some value in comparing two datasets collected in perfectly identical conditions to see which crystal is better and it may predict to some extent what R-values you might expect. Otherwise, it's unreliable. Given that it's been 15 years since this was pointed out in no less than Nature group magazine, and we still hear that Rmerge should decide resolution cutoff, chances are increasingly slim that I will personally see the dethroning of that other major oppressor, R-value. On Fri, 2012-06-01 at 10:59 -0700, aaleshin wrote: Please excuse my ignorance, but I cannot understand why Rmerge is unreliable for estimation of the resolution? I mean, from a theoretical point of view, 1/sigma is indeed a better criterion, but it is not obvious from a practical point of view. 1/sigma depends on a method for sigma estimation, and so same data processed by different programs may have different 1/sigma. Moreover, HKL2000 allows users to adjust sigmas manually. Rmerge estimates sigmas from differences between measurements of same structural factor, and hence is independent of our preferences. But, it also has a very important ability to validate consistency of the merged data. If my crystal changed during the data collection, or something went wrong with the diffractometer, Rmerge will show it immediately, but 1/sigma will not. So, please explain why should we stop using Rmerge as a criterion of data resolution? Alex Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Road La Jolla, California 92037 On Jun 1, 2012, at 5:07 AM, Ian Tickle wrote: On 1 June 2012 03:22, Edward A. Berry ber...@upstate.edu wrote: Leo will probably answer better than I can, but I would say I/SigI counts only the present reflection, so eliminating noise by anisotropic truncation should improve it, raising the average I/SigI in the last shell. We always include unmeasured reflections with I/sigma(I) = 0 in the calculation of the mean I/sigma(I) (i.e. we divide the sum of I/sigma(I) for measureds by the predicted total no of reflections incl unmeasureds), since for unmeasureds I is (almost) completely unknown and therefore sigma(I) is effectively infinite (or at least finite but large since you do have some idea of what range I must fall in). A shell with I/sigma(I) = 2 and 50% completeness clearly doesn't carry the same information content as one with the same I/sigma(I) and 100% complete; therefore IMO it's very misleading to quote I/sigma(I) including only the measured reflections. This also means we can use a single cut-off criterion (we use mean I/sigma(I) 1), and we don't need another arbitrary cut-off criterion for completeness. As many others seem to be doing now, we don't use Rmerge, Rpim etc as criteria to estimate resolution, they're just too unreliable - Rmerge is indeed dead and buried! Actually a mean value of I/sigma(I) of 2 is highly statistically significant, i.e. very unlikely to have arisen by chance variations, and the significance threshold for the mean must be much closer to 1 than to 2. Taking an average always increases the statistical significance, therefore it's not valid to compare an _average_ value of I/sigma(I) = 2 with a _single_ value of I/sigma(I) = 3 (taking 3 sigma as the threshold of statistical significance of an individual measurement): that's a case of comparing apples with pears. In other words in the outer shell you would need a lot of highly significant individual values 3 to attain an overall average of 2 since the majority of individual values will be 1. F/sigF is expected to be better than I/sigI because dx^2 = 2Xdx, dx^2/x^2 = 2dx/x, dI/I = 2* dF/F (or approaches that in the limit . . .)
Re: [ccp4bb] Death of Rmerge
Let's say you collect data (or rather indices) to 1.4 Ang but the real resolution is 2.8 Ang and you use all the data in refinement with no resolution cut-off, so there are 8 times as many data. Then your 15 mins becomes 2 hours - is that still acceptable? It's unlikely that you'll see any difference in the results so was all that extra computing worth the effort? Now work out the total number of pixels in one of your datasets (i.e. no of pixels per image times no of images). Divide that by the no of reflections in the a.u. and multiply by 15 mins (it's probably in the region of 400 days!): still acceptable? Again it's unlikely you'll see any significant difference in the results (assuming you only use the Bragg spots), so again was it worth it? What matters in terms of information content is not the absolute intensity but the ratio intensity / (expected intensity). As the data get weaker at higher d* I falls off, but so does I and the ratio I / I becomes progressively more unreliable at determining the information content. So a zero I when the other intensities in the same d* shell are strong is indeed a powerful constraint (this I suspect is what Wang meant), however if the other intensities in the shell are also all zero it tells you next to nothing. -- Ian On 1 June 2012 20:03, Jacob Keller j-kell...@fsm.northwestern.edu wrote: I don't think any data should be discarded, and I think that although we are not there yet, refinement should work directly with the images, iterating back and forth through all the various levels of data processing. As I think was pointed out by Wang, even an intensity of 0 provides information placing limits on the possible true values of that reflection. It seems that the main reason data were discarded historically was because of the limitations of (under)grad students going through multiple layers of films, evaluating intensities for each spot, or other similar processing limits, most of which are not really applicable today. A whole iterated refinement protocol now takes, what, 15 minutes? Jacob On Fri, Jun 1, 2012 at 1:29 PM, Ed Pozharski epozh...@umaryland.edu wrote: http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html http://scripts.iucr.org/cgi-bin/paper?S0021889800018227 Just collect 360 sweep instead of 180 on a non-decaying crystal and see Rmerge go up due to increase in multiplicity (and enough with redundancy term - the extra data is not really *redundant*). Is your resolution worse or better? This has been argued over before. Rmerge has some value in comparing two datasets collected in perfectly identical conditions to see which crystal is better and it may predict to some extent what R-values you might expect. Otherwise, it's unreliable. Given that it's been 15 years since this was pointed out in no less than Nature group magazine, and we still hear that Rmerge should decide resolution cutoff, chances are increasingly slim that I will personally see the dethroning of that other major oppressor, R-value. On Fri, 2012-06-01 at 10:59 -0700, aaleshin wrote: Please excuse my ignorance, but I cannot understand why Rmerge is unreliable for estimation of the resolution? I mean, from a theoretical point of view, 1/sigma is indeed a better criterion, but it is not obvious from a practical point of view. 1/sigma depends on a method for sigma estimation, and so same data processed by different programs may have different 1/sigma. Moreover, HKL2000 allows users to adjust sigmas manually. Rmerge estimates sigmas from differences between measurements of same structural factor, and hence is independent of our preferences. But, it also has a very important ability to validate consistency of the merged data. If my crystal changed during the data collection, or something went wrong with the diffractometer, Rmerge will show it immediately, but 1/sigma will not. So, please explain why should we stop using Rmerge as a criterion of data resolution? Alex Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Road La Jolla, California 92037 On Jun 1, 2012, at 5:07 AM, Ian Tickle wrote: On 1 June 2012 03:22, Edward A. Berry ber...@upstate.edu wrote: Leo will probably answer better than I can, but I would say I/SigI counts only the present reflection, so eliminating noise by anisotropic truncation should improve it, raising the average I/SigI in the last shell. We always include unmeasured reflections with I/sigma(I) = 0 in the calculation of the mean I/sigma(I) (i.e. we divide the sum of I/sigma(I) for measureds by the predicted total no of reflections incl unmeasureds), since for unmeasureds I is (almost) completely unknown and therefore sigma(I) is effectively infinite (or at least finite but large since you do have some idea of what range I must fall in). A shell with I/sigma(I) = 2 and 50% completeness clearly doesn't carry the same information
Re: [ccp4bb] Death of Rmerge
Hi, as we reported in our paper in Table 1 (actually Supplementary Table 1), at the end of Scaling 2, completeness in the outer shell after aniso truncation was 54%. Whilst 96% completeness and I/sigma 0.8 is of course before aniso truncation. I/sigma after truncation would be higher, but it is not clear to me how to calculate that number exactly, since aniso truncation is done post data scaling. One could of course re-process images in Mosflm with applied aniso limits and then scale data, but that would not be exactly the same. From many trials with strongly anisotropic data we found that for map calculation and refinement it is best to cut data anisotropically where F/sigma is approaching 2.5-2.7 in each direction, as long as completeness in the outer shell remains above 50% or so. Usually the highest useful resolution is also where the correlation coefficient between random half-data-set estimates of intensities in SCALA falls below about 0.5 (as advocated by Phil Evans, I think). CC seems to be less affected by anisotropy (in this case it reached 0.5 at 3.0 angstrom, which was another criterion to cut data at 3.0). HTH. Leo I am little curious about the anisotropically truncated data for 3RKO: Percent Possible(All) 96.0 Mean I Over Sigma(Observed) 0.8 In the supplementary table of the nature paper it was made clear that this 3.16-3.0A, I/sigmaI=0.8 and Rmerge=1.216 shell was the outer shell of the anisotropically truncated data. The authors did also report the isotropically truncated resolution to be 3.2A with I/sigmaI=1.3 and Rmerge=73%. The authors also stated in the main text that the best native data set was anisotropically scaled and truncated to 3.4 Å, 3.0 Å and 3.0 Å resolution, where the F/σ ratio drops to ~2.6–2.8 along the a*, b* and c* axes, respectively (scaling 2, Supplementary Table 1) My question is, is the I/sigmaI=0.8 a consequence of many reflections with nearly 0 I/sigmaI being included in the calculation? Then what does the 96% completeness mean? Does it mean that 96% completeness in the spherical shell of 3.16-3.0A was achieved, by including a great number of I=0 reflections? Zhijie
Re: [ccp4bb] Death of Rmerge
Let's say you collect data (or rather indices) to 1.4 Ang but the real resolution is 2.8 Ang and you use all the data in refinement with no resolution cut-off, so there are 8 times as many data. Then your 15 mins becomes 2 hours - is that still acceptable? It's unlikely that you'll see any difference in the results so was all that extra computing worth the effort? Now work out the total number of pixels in one of your datasets (i.e. no of pixels per image times no of images). Divide that by the no of reflections in the a.u. and multiply by 15 mins (it's probably in the region of 400 days!): still acceptable? Again it's unlikely you'll see any significant difference in the results (assuming you only use the Bragg spots), so again was it worth it? What matters in terms of information content is not the absolute intensity but the ratio intensity / (expected intensity). As the data get weaker at higher d* I falls off, but so does I and the ratio I / I becomes progressively more unreliable at determining the information content. So a zero I when the other intensities in the same d* shell are strong is indeed a powerful constraint (this I suspect is what Wang meant), however if the other intensities in the shell are also all zero it tells you next to nothing. -- Ian I envisioned a process of iteration through the various stages of processing, so still using integration, scaling, etc. to reduce data before refinement, but maybe feeding back model-based information to inform the processing of the images. Something like, Refmac says to Mosflm: kill frames 1100-1200: they're too radiation-damaged. But I like your idea of using all the pixels--that would be the ultimate, wouldn't it! Actually, the best would be to have the refinement already going when collecting data, and informing which frames to take, and for how long! In a couple years that too will take no time at all, but then again, we'll probably have atomic-precision real-time in vivo microscopes by then anyway, and crystallography will have become an (interesting!) historical curiosity... JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
