Re: [ccp4bb] aimless outputs mean intensities for friedel pairs
Indeed, centric reflections should have no anomalous signal after merging
Phil
Sent from my iPhone
> On 31 Mar 2020, at 05:48, Kevin Jude wrote:
>
>
> I've had two more helpful responses to this off-list. My crystal is P43212,
> so there are large swaths of centric reflections that I was looking at. And
> indeed, {18,1,1} is not the first reflection with anomalous differences if I
> look more carefully. Different sorting of the outputs by phenix and aimless
> masked that result for me. Thanks to those who responded for the help and for
> the chance to dive into the International Tables.
>
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
>
>
>> On Mon, Mar 30, 2020 at 8:20 PM Kevin Jude wrote:
>> Thanks Reza. Changing the rejection criteria didn't have any effect, but I
>> tried xdsconv and got what looked like the same result - ie, DANO = 0. That
>> got me started looking at more reflections, and if I make it all the way
>> down to {18,1,1) there's suddenly a switch and anomalous differences are
>> present for the remaining reflections (which are sorted by increasing h, k,
>> l). It turns out the same thing was happening in aimless. This seems strange
>> since it isn't in accord with what I saw in CORRECT.LP, namely significant
>> anomalous signal in the lower resolution shells, and it couldn't be
>> explained away by a wedge of missing Friedel mates.
>>
>> Finally, I decided to see what happens if I used Phenix's reflection file
>> editor to convert XDS_ASCII.HKL to mtz, and. . .it seems to work just fine.
>> So I suppose my problem of getting from here to there is solved, though the
>> puzzle remains.
>>
>> --
>> Kevin Jude, PhD
>> Structural Biology Research Specialist, Garcia Lab
>> Howard Hughes Medical Institute
>> Stanford University School of Medicine
>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>> Phone: (650) 723-6431
>>
>>
>>> On Mon, Mar 30, 2020 at 6:51 PM Rezaul Karim wrote:
>>> Hi Kevin,
>>> Just a thought, guidance is left to the experts. Since the aimless reports
>>> significant anomalous signal default anomalous rejection criteria most
>>> likely is too strict for this run. Changing the default "reject 6 all -8"
>>> value to loosen the rejection criteria might give some clue whether this is
>>> the case. Another alternative is xdsconv. Any advantage of using pointless
>>> and aimless instead of xdsconv for your purpose?
>>>
>>> Thanks,
>>> Reza
>>>
>>> Md. Rezaul Karim (Reza)
>>> Ph.D. candidate, PhD Program in Integrated Biomedical Sciences
>>> Department of Molecular Medicine
>>> Morsani College of Medicine
>>> University of South Florida
>>> Schonbrunn lab, Moffitt Cancer Center
>>> Tampa, FL
>>> E-mail: reza...@yahoo.com, rez...@usf.edu
>>> Phone: +1-954-937-8487
>>> ORCID: https://orcid.org/-0002-0424-127X
>>> LinkedIn: https://www.linkedin.com/in/reza092
>>>
>>>
>>>
>>> On Monday, March 30, 2020, 7:12:33 PM EDT, Kevin Jude
>>> wrote:
>>>
>>>
>>> Hi all,
>>> I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz via
>>> pointless and aimless. Everything looks good through pointless, as far as I
>>> understand:
>>> xds reports significant anomalous correlation in CORRECT.LP
>>>
>>> Inspection of the mtz output from pointless shows that (+) and (-)
>>> reflections are recorded using separate ISYM flags (column 4):
>>>
>>> LIST OF REFLECTIONS
>>> ===
>>>
>>> 0 0 71 902 1.68 1.43 0.91 1230.80
>>>1155.20423.20 0.04 0.00
>>>
>>> 0 0 72 2 1.21 1.68 0.90 1231.40
>>>1155.10243.20 0.04 0.00
>>>
>>> 0 0 81 902 88.18 3.70 1.00 1230.70
>>>1139.50423.36 0.04 0.00
>>>
>>> 0 0 82 2 85.93 3.86 0.99 1231.50
>>>1139.30243.36 0.04 0.00
>>> ...
>>>
>>> But when I run aimless as:
>>>
>>> $ aimless hklin ds5_5_E1_pointless.mtz hklout ds5_5_E1_aimless.mtz
>>> <>> onlymerge
>>> anom on
>>> reso 2.5
>>> end
>>> eof
>>>
>>> the output mtz file has identical values for IMEAN, I(+), and I(-), despite
>>> reporting in the logfile that:
>>> Anomalous flag switched ON in input, strong anomalous signal found
>>> Estimate of the resolution limit for a significant anomalous signal 3.93A,
>>> from the point where the fit drops below threshold 0.15
>>>
>>> Can anybody provide me with some guidance?
>>>
>>> Best wishes
>>> Kevin
>>>
>>> --
>>> Kevin Jude, PhD
>>> Structural Biology Research Specialist, Garcia Lab
>>> Howard Hughes Medical Institute
>>> Stanford University School of Medicine
>>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>>>
Re: [ccp4bb] aimless outputs mean intensities for friedel pairs
I've had two more helpful responses to this off-list. My crystal is P43212,
so there are large swaths of centric reflections that I was looking at. And
indeed, {18,1,1} is not the first reflection with anomalous differences if
I look more carefully. Different sorting of the outputs by phenix and
aimless masked that result for me. Thanks to those who responded for the
help and for the chance to dive into the International Tables.
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
On Mon, Mar 30, 2020 at 8:20 PM Kevin Jude wrote:
> Thanks Reza. Changing the rejection criteria didn't have any effect, but I
> tried xdsconv and got what looked like the same result - ie, DANO = 0. That
> got me started looking at more reflections, and if I make it all the way
> down to {18,1,1) there's suddenly a switch and anomalous differences are
> present for the remaining reflections (which are sorted by increasing h, k,
> l). It turns out the same thing was happening in aimless. This seems
> strange since it isn't in accord with what I saw in CORRECT.LP, namely
> significant anomalous signal in the lower resolution shells, and it
> couldn't be explained away by a wedge of missing Friedel mates.
>
> Finally, I decided to see what happens if I used Phenix's reflection file
> editor to convert XDS_ASCII.HKL to mtz, and. . .it seems to work just fine.
> So I suppose my problem of getting from here to there is solved, though the
> puzzle remains.
>
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
>
>
> On Mon, Mar 30, 2020 at 6:51 PM Rezaul Karim wrote:
>
>> Hi Kevin,
>> Just a thought, guidance is left to the experts. Since the aimless
>> reports significant anomalous signal default anomalous rejection criteria
>> most likely is too strict for this run. Changing the default "reject 6
>> all -8" value to loosen the rejection criteria might give some clue
>> whether this is the case. Another alternative is xdsconv. Any advantage of
>> using pointless and aimless instead of xdsconv for your purpose?
>>
>> Thanks,
>> Reza
>>
>> Md. Rezaul Karim (Reza)
>> Ph.D. candidate, PhD Program in Integrated Biomedical Sciences
>> Department of Molecular Medicine
>> Morsani College of Medicine
>> *University** of South Florida*
>> Schonbrunn lab, Moffitt Cancer Center
>> Tampa, FL
>> E-mail: reza...@yahoo.com, rez...@usf.edu
>> Phone: +1-954-937-8487
>> ORCID: https://orcid.org/-0002-0424-127X
>> LinkedIn: https://www.linkedin.com/in/reza092
>>
>>
>>
>> On Monday, March 30, 2020, 7:12:33 PM EDT, Kevin Jude
>> wrote:
>>
>>
>> Hi all,
>> I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz
>> via pointless and aimless. Everything looks good through pointless, as far
>> as I understand:
>> xds reports significant anomalous correlation in CORRECT.LP
>>
>> Inspection of the mtz output from pointless shows that (+) and (-)
>> reflections are recorded using separate ISYM flags (column 4):
>>
>> LIST OF REFLECTIONS
>> ===
>>
>> 0 0 71 902 1.68 1.43 0.91 1230.80
>>1155.20423.20 0.04 0.00
>>
>> 0 0 72 2 1.21 1.68 0.90 1231.40
>>1155.10243.20 0.04 0.00
>>
>> 0 0 81 902 88.18 3.70 1.00 1230.70
>>1139.50423.36 0.04 0.00
>>
>> 0 0 82 2 85.93 3.86 0.99 1231.50
>>1139.30243.36 0.04 0.00
>> ...
>>
>> But when I run aimless as:
>>
>> $ aimless hklin ds5_5_E1_pointless.mtz hklout ds5_5_E1_aimless.mtz
>> <> onlymerge
>> anom on
>> reso 2.5
>> end
>> eof
>>
>> the output mtz file has identical values for IMEAN, I(+), and I(-),
>> despite reporting in the logfile that:
>> Anomalous flag switched ON in input, strong anomalous signal found
>> Estimate of the resolution limit for a significant anomalous signal
>> 3.93A, from the point where the fit drops below threshold 0.15
>>
>> Can anybody provide me with some guidance?
>>
>> Best wishes
>> Kevin
>>
>> --
>> Kevin Jude, PhD
>> Structural Biology Research Specialist, Garcia Lab
>> Howard Hughes Medical Institute
>> Stanford University School of Medicine
>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>> Phone: (650) 723-6431
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
To unsubscribe from the CCP4BB list, click the following link:
Re: [ccp4bb] aimless outputs mean intensities for friedel pairs
Thanks Reza. Changing the rejection criteria didn't have any effect, but I
tried xdsconv and got what looked like the same result - ie, DANO = 0. That
got me started looking at more reflections, and if I make it all the way
down to {18,1,1) there's suddenly a switch and anomalous differences are
present for the remaining reflections (which are sorted by increasing h, k,
l). It turns out the same thing was happening in aimless. This seems
strange since it isn't in accord with what I saw in CORRECT.LP, namely
significant anomalous signal in the lower resolution shells, and it
couldn't be explained away by a wedge of missing Friedel mates.
Finally, I decided to see what happens if I used Phenix's reflection file
editor to convert XDS_ASCII.HKL to mtz, and. . .it seems to work just fine.
So I suppose my problem of getting from here to there is solved, though the
puzzle remains.
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
On Mon, Mar 30, 2020 at 6:51 PM Rezaul Karim wrote:
> Hi Kevin,
> Just a thought, guidance is left to the experts. Since the aimless reports
> significant anomalous signal default anomalous rejection criteria most
> likely is too strict for this run. Changing the default "reject 6 all -8"
> value to loosen the rejection criteria might give some clue whether this
> is the case. Another alternative is xdsconv. Any advantage of using
> pointless and aimless instead of xdsconv for your purpose?
>
> Thanks,
> Reza
>
> Md. Rezaul Karim (Reza)
> Ph.D. candidate, PhD Program in Integrated Biomedical Sciences
> Department of Molecular Medicine
> Morsani College of Medicine
> *University** of South Florida*
> Schonbrunn lab, Moffitt Cancer Center
> Tampa, FL
> E-mail: reza...@yahoo.com, rez...@usf.edu
> Phone: +1-954-937-8487
> ORCID: https://orcid.org/-0002-0424-127X
> LinkedIn: https://www.linkedin.com/in/reza092
>
>
>
> On Monday, March 30, 2020, 7:12:33 PM EDT, Kevin Jude
> wrote:
>
>
> Hi all,
> I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz via
> pointless and aimless. Everything looks good through pointless, as far as I
> understand:
> xds reports significant anomalous correlation in CORRECT.LP
>
> Inspection of the mtz output from pointless shows that (+) and (-)
> reflections are recorded using separate ISYM flags (column 4):
>
> LIST OF REFLECTIONS
> ===
>
> 0 0 71 902 1.68 1.43 0.91 1230.80
>1155.20423.20 0.04 0.00
>
> 0 0 72 2 1.21 1.68 0.90 1231.40
>1155.10243.20 0.04 0.00
>
> 0 0 81 902 88.18 3.70 1.00 1230.70
>1139.50423.36 0.04 0.00
>
> 0 0 82 2 85.93 3.86 0.99 1231.50
>1139.30243.36 0.04 0.00
> ...
>
> But when I run aimless as:
>
> $ aimless hklin ds5_5_E1_pointless.mtz hklout ds5_5_E1_aimless.mtz
> < onlymerge
> anom on
> reso 2.5
> end
> eof
>
> the output mtz file has identical values for IMEAN, I(+), and I(-),
> despite reporting in the logfile that:
> Anomalous flag switched ON in input, strong anomalous signal found
> Estimate of the resolution limit for a significant anomalous signal
> 3.93A, from the point where the fit drops below threshold 0.15
>
> Can anybody provide me with some guidance?
>
> Best wishes
> Kevin
>
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] aimless outputs mean intensities for friedel pairs
Hi Kevin,Just a thought, guidance is left to the experts. Since the aimless reports significant anomalous signal default anomalous rejection criteria most likely is too strict for this run. Changing the default "reject 6 all -8" value to loosen the rejection criteria might give some clue whether this is the case. Another alternative is xdsconv. Any advantage of using pointless and aimless instead of xdsconv for your purpose? Thanks,Reza Md. Rezaul Karim (Reza) Ph.D. candidate, PhD Program in Integrated Biomedical SciencesDepartment of Molecular MedicineMorsani College of MedicineUniversity of South Florida Schonbrunn lab, Moffitt Cancer CenterTampa, FLE-mail: reza...@yahoo.com, rezaul@usf.eduPhone: +1-954-937-8487ORCID: https://orcid.org/-0002-0424-127X LinkedIn: https://www.linkedin.com/in/reza092 On Monday, March 30, 2020, 7:12:33 PM EDT, Kevin Jude wrote: Hi all,I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz via pointless and aimless. Everything looks good through pointless, as far as I understand:xds reports significant anomalous correlation in CORRECT.LP Inspection of the mtz output from pointless shows that (+) and (-) reflections are recorded using separate ISYM flags (column 4): LIST OF REFLECTIONS === 0 0 7 1 902 1.68 1.43 0.91 1230.80 1155.20 423.20 0.04 0.00 0 0 7 2 2 1.21 1.68 0.90 1231.40 1155.10 243.20 0.04 0.00 0 0 8 1 902 88.18 3.70 1.00 1230.70 1139.50 423.36 0.04 0.00 0 0 8 2 2 85.93 3.86 0.99 1231.50 1139.30 243.36 0.04 0.00... But when I run aimless as: $ aimless hklin ds5_5_E1_pointless.mtz hklout ds5_5_E1_aimless.mtz
[ccp4bb] aimless outputs mean intensities for friedel pairs
Hi all, I am trying to merge and convert reflections from XDS_ASCII.HKL to mtz via pointless and aimless. Everything looks good through pointless, as far as I understand: xds reports significant anomalous correlation in CORRECT.LP Inspection of the mtz output from pointless shows that (+) and (-) reflections are recorded using separate ISYM flags (column 4): LIST OF REFLECTIONS === 0 0 71 902 1.68 1.43 0.91 1230.80 1155.20423.20 0.04 0.00 0 0 72 2 1.21 1.68 0.90 1231.40 1155.10243.20 0.04 0.00 0 0 81 902 88.18 3.70 1.00 1230.70 1139.50423.36 0.04 0.00 0 0 82 2 85.93 3.86 0.99 1231.50 1139.30243.36 0.04 0.00 ... But when I run aimless as: $ aimless hklin ds5_5_E1_pointless.mtz hklout ds5_5_E1_aimless.mtz
