Re: [ccp4bb] Rmeas in DIALS?
Hi Graeme, > On 1 Jul 2021, at 14:21, Winter, Graeme (DLSLtd,RAL,LSCI) > wrote: > > Total observations 1432839600 559 > Total unique 418512397 494 > Assuming spacegroup: P 41 21 2 > Other likely alternatives are: > P 43 21 2 > Unit cell: > 78.580 78.580 36.950 > 90.000 90.000 90.000 Those cell params and no. reflections exactly match the ones from XDS shown in the i2 report. Are the DIALS ones from xia2 different to those shown in the report? Thanks, Huw To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Rmeas in DIALS?
Hi Phil, No argument, you _can_ The question is where it came from in this context, as the outer shell is positive in the text output but somehow -ve in i2 version of the same Unless i2 recalculates merging stats? All the best Graeme On 1 Jul 2021, at 14:52, Phil Evans mailto:p...@mrc-lmb.cam.ac.uk>> wrote: You can get a negative Rmeas in a shell where is negative Sent from my iPhone On 1 Jul 2021, at 14:21, Winter, Graeme (DLSLtd,RAL,LSCI) mailto:graeme.win...@diamond.ac.uk>> wrote: Thanks for sending the logs Looking at the output the negative R values don’t come from xia2 directly For AUTOMATIC/DEFAULT/NATIVE OverallLow High High resolution limit 1.012.741.01 Low resolution limit 36.95 36.971.03 Completeness 68.672.216.3 Multiplicity3.4 4.0 1.1 I/sigma 6.811.0 0.6 Rmerge(I) 0.127 0.131 1.543 Rmerge(I+/-) 0.121 0.127 1.173 Rmeas(I) 0.141 0.147 2.162 Rmeas(I+/-) 0.145 0.151 1.659 Rpim(I) 0.059 0.062 1.512 Rpim(I+/-)0.078 0.079 1.173 CC half 0.985 0.971 0.149 Wilson B factor 11.910 Anomalous completeness 45.757.6 1.8 Anomalous multiplicity 2.1 2.5 1.0 Anomalous correlation-0.106 -0.135 0.000 Anomalous slope 0.921 dF/F 0.079 dI/s(dI) 0.699 Total observations 1432839600 559 Total unique 418512397 494 Assuming spacegroup: P 41 21 2 Other likely alternatives are: P 43 21 2 Unit cell: 78.580 78.580 36.950 90.000 90.000 90.000 While a 1990’s reviewer would have a hard time with those merging stats, I have seen worse and they seem internally consistent I wonder, is ccp4i2 doing something itself which arrives at those numbers? i2 devs - thoughts? Thanks Graeme On 1 Jul 2021, at 05:49, Winter, Graeme (DLSLtd,RAL,LSCI) mailto:graeme.win...@diamond.ac.uk>> wrote: Something odd happening there - please could you send the text log off list? i.e. xia2.txt Thanks Graeme On 1 Jul 2021, at 00:58, Murpholino Peligro mailto:murpholi...@gmail.com>> wrote: Why Rmeas is negative in DIALS output? Thanks To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation
Re: [ccp4bb] Rmeas in DIALS?
You can get a negative Rmeas in a shell where is negative Sent from my iPhone > On 1 Jul 2021, at 14:21, Winter, Graeme (DLSLtd,RAL,LSCI) > wrote: > > Thanks for sending the logs > > Looking at the output the negative R values don’t come from xia2 directly > > For AUTOMATIC/DEFAULT/NATIVE OverallLow High > High resolution limit 1.012.741.01 > Low resolution limit 36.95 36.971.03 > Completeness 68.672.216.3 > Multiplicity3.4 4.0 1.1 > I/sigma 6.811.0 0.6 > Rmerge(I) 0.127 0.131 1.543 > Rmerge(I+/-) 0.121 0.127 1.173 > Rmeas(I) 0.141 0.147 2.162 > Rmeas(I+/-) 0.145 0.151 1.659 > Rpim(I) 0.059 0.062 1.512 > Rpim(I+/-)0.078 0.079 1.173 > CC half 0.985 0.971 0.149 > Wilson B factor 11.910 > Anomalous completeness 45.757.6 1.8 > Anomalous multiplicity 2.1 2.5 1.0 > Anomalous correlation-0.106 -0.135 0.000 > Anomalous slope 0.921 > dF/F 0.079 > dI/s(dI) 0.699 > Total observations 1432839600 559 > Total unique 418512397 494 > Assuming spacegroup: P 41 21 2 > Other likely alternatives are: > P 43 21 2 > Unit cell: > 78.580 78.580 36.950 > 90.000 90.000 90.000 > > While a 1990’s reviewer would have a hard time with those merging stats, I > have seen worse and they seem internally consistent > > I wonder, is ccp4i2 doing something itself which arrives at those numbers? > > i2 devs - thoughts? > > Thanks Graeme > >>> On 1 Jul 2021, at 05:49, Winter, Graeme (DLSLtd,RAL,LSCI) >>> wrote: >>> >>> Something odd happening there - please could you send the text log off >>> list? i.e. xia2.txt >>> >>> Thanks Graeme >>> >>> On 1 Jul 2021, at 00:58, Murpholino Peligro wrote: >>> >>> Why Rmeas is negative in DIALS output? >>> >>> >>> Thanks >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >>> >>> >> >> >> -- >> >> This e-mail and any attachments may contain confidential, copyright and or >> privileged material, and are for the use of the intended addressee only. If >> you are not the intended addressee or an authorised recipient of the >> addressee please notify us of receipt by returning the e-mail and do not >> use, copy, retain, distribute or disclose the information in or attached to >> the e-mail. >> Any opinions expressed within this e-mail are those of the individual and >> not necessarily of Diamond Light Source Ltd. >> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >> attachments are free from viruses and we cannot accept liability for any >> damage which you may sustain as a result of software viruses which may be >> transmitted in or with the message. >> Diamond Light Source Limited (company no. 4375679). Registered in England >> and Wales with its registered office at Diamond House, Harwell Science and >> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> > > > > -- > > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not use, > copy, retain, distribute or disclose the information in or attached to the > e-mail. > Any opinions expressed within this e-mail are those of the individual and not > necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England and > Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
Re: [ccp4bb] Rmeas in DIALS?
Thanks for sending the logs Looking at the output the negative R values don’t come from xia2 directly For AUTOMATIC/DEFAULT/NATIVE OverallLow High High resolution limit 1.012.741.01 Low resolution limit 36.95 36.971.03 Completeness 68.672.216.3 Multiplicity3.4 4.0 1.1 I/sigma 6.811.0 0.6 Rmerge(I) 0.127 0.131 1.543 Rmerge(I+/-) 0.121 0.127 1.173 Rmeas(I) 0.141 0.147 2.162 Rmeas(I+/-) 0.145 0.151 1.659 Rpim(I) 0.059 0.062 1.512 Rpim(I+/-)0.078 0.079 1.173 CC half 0.985 0.971 0.149 Wilson B factor 11.910 Anomalous completeness 45.757.6 1.8 Anomalous multiplicity 2.1 2.5 1.0 Anomalous correlation-0.106 -0.135 0.000 Anomalous slope 0.921 dF/F 0.079 dI/s(dI) 0.699 Total observations 1432839600 559 Total unique 418512397 494 Assuming spacegroup: P 41 21 2 Other likely alternatives are: P 43 21 2 Unit cell: 78.580 78.580 36.950 90.000 90.000 90.000 While a 1990’s reviewer would have a hard time with those merging stats, I have seen worse and they seem internally consistent I wonder, is ccp4i2 doing something itself which arrives at those numbers? i2 devs - thoughts? Thanks Graeme On 1 Jul 2021, at 05:49, Winter, Graeme (DLSLtd,RAL,LSCI) mailto:graeme.win...@diamond.ac.uk>> wrote: Something odd happening there - please could you send the text log off list? i.e. xia2.txt Thanks Graeme On 1 Jul 2021, at 00:58, Murpholino Peligro mailto:murpholi...@gmail.com>> wrote: Why Rmeas is negative in DIALS output? Thanks To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Rmeas in DIALS?
Something odd happening there - please could you send the text log off list? i.e. xia2.txt Thanks Graeme On 1 Jul 2021, at 00:58, Murpholino Peligro mailto:murpholi...@gmail.com>> wrote: Why Rmeas is negative in DIALS output? Thanks To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
