[ccp4bb] unique reflections vs unique observations
Dear CCP4 users, I am a bit confused about the use of these terms in regards to structure refinement statistics. When I process my data with SCALA, the program outputs statistics in terms of total and unique numbers of observations. However, when I use the MTZ files with REFMAC, the final PDB file has number of reflections. These values are of similar magnitude, but not identical. The issue is even more complicated when I look at tables of statistics between different journals. Authors often report unique reflections or unique observations. My questions are: 1) Are these two terms interchangable? 2) Are they relevant to the different stages of processing (e.g. data collection vs structure refinement)? 3) How do I rationalize the difference between the two values? I have read some of the widely used textbooks, but I am still confused when looking at publications. Any comments would be highly appreciated! Kind regards, Naveed Nadvi Faculty of Pharmacy, University of Sydney.
Re: [ccp4bb] unique reflections vs unique observations
Dear Naveed, The situation can indeed be a bit confusing. The term observations is actually used with two different senses in SCALA. The first is in text such as the following: Number of observations read :62154 Number of unique reflections read: 5108 Number of observations output: 4922 Number of outliers rejected : 26 Number of observations rejected on Emax limit:0 Number of observations outside resolution limits :0 (observations outside resolution limits are omitted from the output file) In this case, each part of a partially recorded reflection (those that span several images) is counted as a separate observation, so for example if a reflection spans 3 images it will have 3 observation. However, in the summary at the end of SCALA it gives: Overall InnerShell OuterShell Total number of observations 23342 759 2493 Total number unique 4922 173 546 This is from the same logfile, but here the total number of observations is AFTER the components of partials have been added together, so the number is smaller. However the number of unique reflections is the same. Typically, number of observations refers to this latter number rather than the former. In a typical Table 1, the number of reflections would be the number of unique reflections (ie after merging symmetry mates) while I feel that the number of observations should be reserved for the total number of reflections measured (before merging symmetry mates). Very often the multiplicity is also given in Table 1, which allows a rough estimate of the total number of observations if this is not given explicitly. Note also that some reflections output by SCALA can be rejected at the TRUNCATE step (those that are too negative and possibly E value outliers, although the latter are normally rejected by SCALA). Thus the number you see in the MTZ file as used by REFMAC may have fewer reflections than those reported by SCALA as unique reflections. Strictly speaking, the Number of reflections in Table 1 should be those output by TRUNCATE (if used) rather than those reported in the SCALA logfile, but I think many people use the value given by SCALA. I hope this helps clarify things a bit. Best wishes, Andrew Leslie Dear CCP4 users, I am a bit confused about the use of these terms in regards to structure refinement statistics. When I process my data with SCALA, the program outputs statistics in terms of total and unique numbers of observations. However, when I use the MTZ files with REFMAC, the final PDB file has number of reflections. These values are of similar magnitude, but not identical. The issue is even more complicated when I look at tables of statistics between different journals. Authors often report unique reflections or unique observations. My questions are: 1) Are these two terms interchangable? 2) Are they relevant to the different stages of processing (e.g. data collection vs structure refinement)? 3) How do I rationalize the difference between the two values? I have read some of the widely used textbooks, but I am still confused when looking at publications. Any comments would be highly appreciated! Kind regards, Naveed Nadvi Faculty of Pharmacy, University of Sydney.
Re: [ccp4bb] unique reflections vs unique observations
I am aware that some programs report interesting numbers. In addition to what Andrew wrote about resolution cutoffs and truncated reflections, I'd like to mention another issue with systematically absent reflections. The number of observations or reflections that come from an integration program are fed into a scaling program. However, the integration program may use a different space group than the scaling program. I am aware that in HKL systematically absent reflections are counted as observations when given to the scaling program SCALEPACK, and are reported in the log file as a unique reflection, but do not appear in the output *.sca file. For example, when the integration program uses spacegroup P4 to integrate, then the user scales in spacegroup P4(1)2(1)2. What happens to the (0 0 5), (0 0 6), (0 0 7), (0 0 9), (0 11 0), and other systematically absent reflections in P4(1)2(1)2 that are passed from the integration program to the scaliing program? I can tell you that they disappear from the output file, but appear in the total number of observations in the log file. So if the input file to scaling has 169 systematically absence observations that when reduced to unique reflections yield 69 unique reflections, then SCALEPACK will report 169 extra input observations and 69 extra output unique reflections than are present. Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Naveed A Nadvi [nnad2...@uni.sydney.edu.au] Sent: Sunday, April 15, 2012 3:06 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unique reflections vs unique observations Dear CCP4 users, I am a bit confused about the use of these terms in regards to structure refinement statistics. When I process my data with SCALA, the program outputs statistics in terms of total and unique numbers of observations. However, when I use the MTZ files with REFMAC, the final PDB file has number of reflections. These values are of similar magnitude, but not identical. The issue is even more complicated when I look at tables of statistics between different journals. Authors often report unique reflections or unique observations. My questions are: 1) Are these two terms interchangable? 2) Are they relevant to the different stages of processing (e.g. data collection vs structure refinement)? 3) How do I rationalize the difference between the two values? I have read some of the widely used textbooks, but I am still confused when looking at publications. Any comments would be highly appreciated! Kind regards, Naveed Nadvi Faculty of Pharmacy, University of Sydney.
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[ccp4bb] Real Space Refine Zone for Ligand
Dear Crystallographers, After one round of refinement (restrained refinement) with ligand, I inport the .cif file through '-Import CIF Dictionary' into Coot. But when I am going for '-Real Space Refine Zone' for the ligand, its showing Refinement set up failure. Failed to find restrained for: LIG. Please suggest. Thanks and Regards, Dipankar This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] software to generate protein topology diagram like those available at PDBsum webserver
Dear All, Thanks to Herb, John, Simanshu, and Anu for link: http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html to generate PDBsum like topology diagrams. Partha On Sun, Apr 15, 2012 at 8:08 PM, Parthasarathy Sampathkumar spart...@gmail.com wrote: Dear All, I would like to generate a topology diagram similar to the ones available for deposited entries at the PDBsum webpage (attached one such diagram here for reference) for a new structure. Is this program is available for download? I am aware of TopDraw. However, I am trying to analyze a ~850 a.a. structure. So, some automation would be helpful. Thanks in advance for your help. Best wishes, Partha
