Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi James, I would say that 0.333 (in a scientific context) implies that I am confident about this number up to the third decimal point, i.e. 0.3325 = x = 0.3334. This gives you an idea of the precision. 1/3 is not a scientific format, but a mathematical one, unless for some constraint you know that value is exactly 1/3, then there is no error associated with it. Cheers, Tim On 07/23/2014 09:57 PM, James Holton wrote: Where is it written that compactness of representation and accuracy/precision are the same thing? Is 1/3 more or less precise than 0.333 ? If mmCIF were a binary floating-point format file, there would be more decimal places in the precision of the stored value for the unit cell, despite fitting into only 4 bytes instead of the 13 bytes of text some seem offended to see below. Would that be better? Or worse? -James Holton MAD Scientist On 7/22/2014 4:01 AM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org mailto:b...@ruppweb.org b...@hofkristallamt.org mailto:b...@hofkristallamt.org http://www.ruppweb.org/ --- - -- - -- 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/ iD8DBQFT0NofUxlJ7aRr7hoRAjEHAKDHJB/iHYgx6qJyr/k3U5TI5y6YSACguJli rWda+amIYdVWnT40WGw8dPA= =taoT -END PGP SIGNATURE-
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
Although Zby's remarks re precision are beyond my original bewilderment about listed zepto-meter range digits (sans precision measure), I wonder whether the argument that we have so many data and thus a quite high precision (n.b. not accuracy) can be attained, is perhaps somewhat optimistic. What we measure or assign as a 'spot' is largely predetermined by various integration, profile, box selection, etc, parameters and whatever does not fit that spot model cannot be properly accounted for. I therefore argue that any precision estimate is probably biased towards optimism by the limitations of the particular reflection spot model. Most reflection 'spots' are dirty little creatures with tentacles, fuzz, bumps, etc In the listed mmCIF case the senseless printing of double precision format was actually the simple point to be made. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zbyszek Otwinowski Sent: Dienstag, 22. Juli 2014 23:49 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein Crystallography challenges Standard Model precision The least-square procedure for unit cell parameter refinement provides very precise estimates of uncertainty. Why they are so precise? Because we use many thousands of unmerged reflections to determine the precision 1 to 6 parameters (unit cell parameters). However, although error propagation through the least squares provides precision of about 0.001 A, or better in some cases, this is only precision not accuracy, and the precision is calculated typically with respect to the unit cell parameters averaged across the exposed volume of a crystal. In practice, the range of unit cell parameters within a crystal can be quite broad, and when we consider accuracy it is not clear, which unit cell parameters should be a reference point. Typically, the distribution of unit cell parameters in a crystal will not follow Gaussian distribution. Therefore, the accuracy of unit cell parameters determination is not well defined, even when we know the experimental conditions very well and propagate experimental uncertainties correctly. Variability of unit cell parameters can be quite high for data sets from different samples. However, description of this variability is typically not related to the very high precision of determination of unit cell parameters for an individual sample. Zbyszek On 07/22/2014 12:33 PM, Tim Gruene wrote: Dear Zbyszek, when you optimise a set of parameters against a set of data, I guess you can also provide their errors. If I understand correctly, this comes with least-squares-routines. I only pointed out that cell errors are listed in the XDS output (provided you refine them, of course). I am sure those errors are well defined. Best wishes, Tim On 07/22/2014 06:53 PM, Zbyszek Otwinowski wrote: Error estimates for the unit cell dimensions in macromolecular crystallography belong to atypical category of uncertainty estimates. Random error contribution in most cases is below 0.001A, so it can be neglected. Wavelength calibration error can be also made very small; however, I do not know how big it is in practice. Goniostat wobble error is taken into account in Scalepack refinement. Crystal-to-detector distance is not used in postrefinement/global refinement. Due to the measurement error being very small, even small variations in unit cell parameters can be detected within cryocooled crystals. These variations almost always are _orders_of_magnitude_larger_ than measurement uncertainty. Current practise is not to investigate the magnitude of the changes in the unit cell parameters, but when beam smaller than crystal is used, observing variations as large as 1A is not unusual. The main question is: what the unit cell uncertainty means? For most samples I could defend to use values: 0.001A, 0.01A, 0.1A and 1A as reasonable, depending on particular point of view. Without defining what the unit cell uncertainty means, publishing its values is pointless. Zbyszek Otwinowski Hi Bernhard, A look at the methods section might give you a clue. Neither XDS nor XSCALE create mmCIF - files (you are talking about mmCIF, not CIF - subtle, but annoying difference), so that the choice is limited. I guess some programmer (rather than a scientist ;-) )used a simple printf commmand for a double precision number so the junk is left over from the memory region or other noise common to conversions. XDS actually prints error estimates for the cell dimensions in CORRECT.LP which could be added to the mmCIF file - a cif (sic!) file, I believe, requires those, by the way and checkCIF would complain about their absence. Cheers, Tim On 07/22/2014 01:01 PM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
Where is it written that compactness of representation and accuracy/precision are the same thing? Is 1/3 more or less precise than 0.333 ? If mmCIF were a binary floating-point format file, there would be more decimal places in the precision of the stored value for the unit cell, despite fitting into only 4 bytes instead of the 13 bytes of text some seem offended to see below. Would that be better? Or worse? -James Holton MAD Scientist On 7/22/2014 4:01 AM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org mailto:b...@ruppweb.org b...@hofkristallamt.org mailto:b...@hofkristallamt.org http://www.ruppweb.org/ ---
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
The representation is simply non-parsimonious. There is no meaning to the zepto-meter digits. Numquam ponenda est pluralitas sine necessitate. BR From: James Holton [mailto:jmhol...@lbl.gov] Sent: Wednesday, July 23, 2014 9:58 PM To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein Crystallography challenges Standard Model precision Where is it written that compactness of representation and accuracy/precision are the same thing? Is 1/3 more or less precise than 0.333 ? If mmCIF were a binary floating-point format file, there would be more decimal places in the precision of the stored value for the unit cell, despite fitting into only 4 bytes instead of the 13 bytes of text some seem offended to see below. Would that be better? Or worse? -James Holton MAD Scientist On 7/22/2014 4:01 AM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta 99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits . Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ ---
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
Greetings all - My interest in the rest of the discussion of experimental precision and error notwithstanding, and at the risk of stating explicitly what some might consider obvious, it seems to me that no one has actually (intentionally) asserted that they have determined the unit cell to 10^-20 meter precision. Rather, I find it far more likely that some program just output the floating point representation of a 3-decimal-place number without a proper 3-decimal-place format string (something like `printf(“%f”, _cell.length_a)` instead of `printf(“%5.3f”, _cell.length_a)`, perhaps). The extra digits are the “noise” of floating point rounding error. Notice the repeating 9’s and 0’s after 3 decimal places in each of the values in question: _cell.entry_id 4c69 _cell.length_a 100.152000427 == 100.152 _cell.length_b 58.3689994812 == 58.369 _cell.length_c 66.5449981689 == 66.545 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 == 99.252 _cell.angle_gamma 90.0 Each of these “extra precise” numbers should simply have been output with only 3 decimal places. But I suppose this still doesn’t answer the original question of *which* program actually needs to be fixed. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jul 23, 2014, at 5:44 PM, Bernhard Rupp hofkristall...@gmail.commailto:hofkristall...@gmail.com wrote: The representation is simply non-parsimonious. There is no meaning to the zepto-meter digits. Numquam ponenda est pluralitas sine necessitate. BR From: James Holton [mailto:jmhol...@lbl.gov] Sent: Wednesday, July 23, 2014 9:58 PM To: b...@hofkristallamt.orgmailto:b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein Crystallography challenges Standard Model precision Where is it written that compactness of representation and accuracy/precision are the same thing? Is 1/3 more or less precise than 0.333 ? If mmCIF were a binary floating-point format file, there would be more decimal places in the precision of the stored value for the unit cell, despite fitting into only 4 bytes instead of the 13 bytes of text some seem offended to see below. Would that be better? Or worse? -James Holton MAD Scientist On 7/22/2014 4:01 AM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits.. Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.orgmailto:b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, A look at the methods section might give you a clue. Neither XDS nor XSCALE create mmCIF - files (you are talking about mmCIF, not CIF - subtle, but annoying difference), so that the choice is limited. I guess some programmer (rather than a scientist ;-) )used a simple printf commmand for a double precision number so the junk is left over from the memory region or other noise common to conversions. XDS actually prints error estimates for the cell dimensions in CORRECT.LP which could be added to the mmCIF file - a cif (sic!) file, I believe, requires those, by the way and checkCIF would complain about their absence. Cheers, Tim On 07/22/2014 01:01 PM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits.. - Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- - -- - -- 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/ iD8DBQFTzk52UxlJ7aRr7hoRAul8AKCHFz/DAoqR7s0fGUp79xx2QlrfCQCeIiiy KXSurhgaQjhguKr9L0/zyVk= =vqGC -END PGP SIGNATURE-
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
I took a look at both the PDB and CIF headers for the coordinates for 4C69 and they have normal looking numbers with three digits following the decimal point. According to the coordinate file header this entry was processed by PDBE. It would be interesting to hear from the PDBE staff if the structure factor file arrived with those numbers or if they were introduced during processing. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Tue, 22 Jul 2014, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta 99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits?. Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ ---
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
Error estimates for the unit cell dimensions in macromolecular crystallography belong to atypical category of uncertainty estimates. Random error contribution in most cases is below 0.001A, so it can be neglected. Wavelength calibration error can be also made very small; however, I do not know how big it is in practice. Goniostat wobble error is taken into account in Scalepack refinement. Crystal-to-detector distance is not used in postrefinement/global refinement. Due to the measurement error being very small, even small variations in unit cell parameters can be detected within cryocooled crystals. These variations almost always are _orders_of_magnitude_larger_ than measurement uncertainty. Current practise is not to investigate the magnitude of the changes in the unit cell parameters, but when beam smaller than crystal is used, observing variations as large as 1A is not unusual. The main question is: what the unit cell uncertainty means? For most samples I could defend to use values: 0.001A, 0.01A, 0.1A and 1A as reasonable, depending on particular point of view. Without defining what the unit cell uncertainty means, publishing its values is pointless. Zbyszek Otwinowski -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, A look at the methods section might give you a clue. Neither XDS nor XSCALE create mmCIF - files (you are talking about mmCIF, not CIF - subtle, but annoying difference), so that the choice is limited. I guess some programmer (rather than a scientist ;-) )used a simple printf commmand for a double precision number so the junk is left over from the memory region or other noise common to conversions. XDS actually prints error estimates for the cell dimensions in CORRECT.LP which could be added to the mmCIF file - a cif (sic!) file, I believe, requires those, by the way and checkCIF would complain about their absence. Cheers, Tim On 07/22/2014 01:01 PM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits.. - Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- - -- - -- 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/ iD8DBQFTzk52UxlJ7aRr7hoRAul8AKCHFz/DAoqR7s0fGUp79xx2QlrfCQCeIiiy KXSurhgaQjhguKr9L0/zyVk= =vqGC -END PGP SIGNATURE- Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
Dear Zbyszek, when you optimise a set of parameters against a set of data, I guess you can also provide their errors. If I understand correctly, this comes with least-squares-routines. I only pointed out that cell errors are listed in the XDS output (provided you refine them, of course). I am sure those errors are well defined. Best wishes, Tim On 07/22/2014 06:53 PM, Zbyszek Otwinowski wrote: Error estimates for the unit cell dimensions in macromolecular crystallography belong to atypical category of uncertainty estimates. Random error contribution in most cases is below 0.001A, so it can be neglected. Wavelength calibration error can be also made very small; however, I do not know how big it is in practice. Goniostat wobble error is taken into account in Scalepack refinement. Crystal-to-detector distance is not used in postrefinement/global refinement. Due to the measurement error being very small, even small variations in unit cell parameters can be detected within cryocooled crystals. These variations almost always are _orders_of_magnitude_larger_ than measurement uncertainty. Current practise is not to investigate the magnitude of the changes in the unit cell parameters, but when beam smaller than crystal is used, observing variations as large as 1A is not unusual. The main question is: what the unit cell uncertainty means? For most samples I could defend to use values: 0.001A, 0.01A, 0.1A and 1A as reasonable, depending on particular point of view. Without defining what the unit cell uncertainty means, publishing its values is pointless. Zbyszek Otwinowski Hi Bernhard, A look at the methods section might give you a clue. Neither XDS nor XSCALE create mmCIF - files (you are talking about mmCIF, not CIF - subtle, but annoying difference), so that the choice is limited. I guess some programmer (rather than a scientist ;-) )used a simple printf commmand for a double precision number so the junk is left over from the memory region or other noise common to conversions. XDS actually prints error estimates for the cell dimensions in CORRECT.LP which could be added to the mmCIF file - a cif (sic!) file, I believe, requires those, by the way and checkCIF would complain about their absence. Cheers, Tim On 07/22/2014 01:01 PM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits.. Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353 -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
The least-square procedure for unit cell parameter refinement provides very precise estimates of uncertainty. Why they are so precise? Because we use many thousands of unmerged reflections to determine the precision 1 to 6 parameters (unit cell parameters). However, although error propagation through the least squares provides precision of about 0.001 A, or better in some cases, this is only precision not accuracy, and the precision is calculated typically with respect to the unit cell parameters averaged across the exposed volume of a crystal. In practice, the range of unit cell parameters within a crystal can be quite broad, and when we consider accuracy it is not clear, which unit cell parameters should be a reference point. Typically, the distribution of unit cell parameters in a crystal will not follow Gaussian distribution. Therefore, the accuracy of unit cell parameters determination is not well defined, even when we know the experimental conditions very well and propagate experimental uncertainties correctly. Variability of unit cell parameters can be quite high for data sets from different samples. However, description of this variability is typically not related to the very high precision of determination of unit cell parameters for an individual sample. Zbyszek On 07/22/2014 12:33 PM, Tim Gruene wrote: Dear Zbyszek, when you optimise a set of parameters against a set of data, I guess you can also provide their errors. If I understand correctly, this comes with least-squares-routines. I only pointed out that cell errors are listed in the XDS output (provided you refine them, of course). I am sure those errors are well defined. Best wishes, Tim On 07/22/2014 06:53 PM, Zbyszek Otwinowski wrote: Error estimates for the unit cell dimensions in macromolecular crystallography belong to atypical category of uncertainty estimates. Random error contribution in most cases is below 0.001A, so it can be neglected. Wavelength calibration error can be also made very small; however, I do not know how big it is in practice. Goniostat wobble error is taken into account in Scalepack refinement. Crystal-to-detector distance is not used in postrefinement/global refinement. Due to the measurement error being very small, even small variations in unit cell parameters can be detected within cryocooled crystals. These variations almost always are _orders_of_magnitude_larger_ than measurement uncertainty. Current practise is not to investigate the magnitude of the changes in the unit cell parameters, but when beam smaller than crystal is used, observing variations as large as 1A is not unusual. The main question is: what the unit cell uncertainty means? For most samples I could defend to use values: 0.001A, 0.01A, 0.1A and 1A as reasonable, depending on particular point of view. Without defining what the unit cell uncertainty means, publishing its values is pointless. Zbyszek Otwinowski Hi Bernhard, A look at the methods section might give you a clue. Neither XDS nor XSCALE create mmCIF - files (you are talking about mmCIF, not CIF - subtle, but annoying difference), so that the choice is limited. I guess some programmer (rather than a scientist ;-) )used a simple printf commmand for a double precision number so the junk is left over from the memory region or other noise common to conversions. XDS actually prints error estimates for the cell dimensions in CORRECT.LP which could be added to the mmCIF file - a cif (sic!) file, I believe, requires those, by the way and checkCIF would complain about their absence. Cheers, Tim On 07/22/2014 01:01 PM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits.. Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353 -- Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
Shouldn't the cell dimensions be identical in the coordinate file and in the structure factor file? In this case they are not. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Tue, 22 Jul 2014, Zbyszek Otwinowski wrote: The least-square procedure for unit cell parameter refinement provides very precise estimates of uncertainty. Why they are so precise? Because we use many thousands of unmerged reflections to determine the precision 1 to 6 parameters (unit cell parameters). However, although error propagation through the least squares provides precision of about 0.001 A, or better in some cases, this is only precision not accuracy, and the precision is calculated typically with respect to the unit cell parameters averaged across the exposed volume of a crystal. In practice, the range of unit cell parameters within a crystal can be quite broad, and when we consider accuracy it is not clear, which unit cell parameters should be a reference point. Typically, the distribution of unit cell parameters in a crystal will not follow Gaussian distribution. Therefore, the accuracy of unit cell parameters determination is not well defined, even when we know the experimental conditions very well and propagate experimental uncertainties correctly. Variability of unit cell parameters can be quite high for data sets from different samples. However, description of this variability is typically not related to the very high precision of determination of unit cell parameters for an individual sample. Zbyszek On 07/22/2014 12:33 PM, Tim Gruene wrote: Dear Zbyszek, when you optimise a set of parameters against a set of data, I guess you can also provide their errors. If I understand correctly, this comes with least-squares-routines. I only pointed out that cell errors are listed in the XDS output (provided you refine them, of course). I am sure those errors are well defined. Best wishes, Tim On 07/22/2014 06:53 PM, Zbyszek Otwinowski wrote: Error estimates for the unit cell dimensions in macromolecular crystallography belong to atypical category of uncertainty estimates. Random error contribution in most cases is below 0.001A, so it can be neglected. Wavelength calibration error can be also made very small; however, I do not know how big it is in practice. Goniostat wobble error is taken into account in Scalepack refinement. Crystal-to-detector distance is not used in postrefinement/global refinement. Due to the measurement error being very small, even small variations in unit cell parameters can be detected within cryocooled crystals. These variations almost always are _orders_of_magnitude_larger_ than measurement uncertainty. Current practise is not to investigate the magnitude of the changes in the unit cell parameters, but when beam smaller than crystal is used, observing variations as large as 1A is not unusual. The main question is: what the unit cell uncertainty means? For most samples I could defend to use values: 0.001A, 0.01A, 0.1A and 1A as reasonable, depending on particular point of view. Without defining what the unit cell uncertainty means, publishing its values is pointless. Zbyszek Otwinowski Hi Bernhard, A look at the methods section might give you a clue. Neither XDS nor XSCALE create mmCIF - files (you are talking about mmCIF, not CIF - subtle, but annoying difference), so that the choice is limited. I guess some programmer (rather than a scientist ;-) )used a simple printf commmand for a double precision number so the junk is left over from the memory region or other noise common to conversions. XDS actually prints error estimates for the cell dimensions in CORRECT.LP which could be added to the mmCIF file - a cif (sic!) file, I believe, requires those, by the way and checkCIF would complain about their absence. Cheers, Tim On 07/22/2014 01:01 PM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits..
