Re: [ccp4bb] How to get Imean/SIGImean from separated anomalous data?
It's quite a change compared to i1, but worth to learn it. On Wed, Mar 14, 2018 at 5:33 PM, Edward A. Berry <ber...@upstate.edu> wrote: > Thanks, that seems to work also, and with lots of nice graphical analysis. > With Task "Import merged data", or all in one go with "convert intensities > to amplitudes" selecting the .cif file as input and option "output Imean > for anomalous data", to run ctruncate on the result. > > But I have a long way to go to get used to I2. It was disconcerting not > being able to set the output filenames, or even find the output files > except by listing files in the project directory. I guess it's a new > paradigm, where you don't need to worry about details like file names and > you identify datasets by internal labels within the gui. And going back to > the finished job, looking at input and options, there was very little > information about exactly what had been done (compared to the detailed > forms in ccp4i). But now I am motivated to learn the new system! > eab > > On 03/14/2018 06:42 AM, Eleanor Dodson wrote: > >> No problem with GUI2.. >> >> Eleanor >> >> On 13 March 2018 at 22:38, Edward A. Berry <ber...@upstate.edu > ber...@upstate.edu>> wrote: >> >> Thanks- that works! >> pdb-redo/tools/cif2cif in.cif out.cif >> eab >> >> >> On 03/13/2018 05:47 PM, Robbie Joosten wrote: >> >> Hi Ed, >> >> The pdb-redo program cif2cif does that. I implemented this >> feature because there was no obvious CCP4 program that did this. You have >> to have your data in mmCIF format though. >> >> Cheers, >> >> Robbie >> >> Sent from my Windows 10 phone >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------ >> > - > - > >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK > CCP4BB@JISCMAIL.AC.UK>> on behalf of Edward A. Berry <ber...@upstate.edu >> <mailto:ber...@upstate.edu>> >> *Sent:* Tuesday, March 13, 2018 10:25:25 PM >> *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> >> *Subject:* [ccp4bb] How to get Imean/SIGImean from separated >> anomalous data? >> >> I want to work with an mmcif file that has I+,sigI+,I-,SigI-; >> in different columns for each reflection (no Imean). >> cif2mtz gives those same columns in the output mtz, with or >> without ANOMALOUS keyword. >> cif2mtz and truncate seem to need the anomalous data as separate >> reflections hkl and -h-k-l in order to calculate Imean or Fmean. What is >> the best way to do this? >> Thanks, >> eab >> >> >>
Re: [ccp4bb] How to get Imean/SIGImean from separated anomalous data?
Thanks, that seems to work also, and with lots of nice graphical analysis.
With Task "Import merged data", or all in one go with "convert intensities to amplitudes"
selecting the .cif file as input and option "output Imean for anomalous data", to run ctruncate on
the result.
But I have a long way to go to get used to I2. It was disconcerting not being
able to set the output filenames, or even find the output files except by
listing files in the project directory. I guess it's a new paradigm, where you
don't need to worry about details like file names and you identify datasets by
internal labels within the gui. And going back to the finished job, looking at
input and options, there was very little information about exactly what had
been done (compared to the detailed forms in ccp4i). But now I am motivated to
learn the new system!
eab
On 03/14/2018 06:42 AM, Eleanor Dodson wrote:
No problem with GUI2..
Eleanor
On 13 March 2018 at 22:38, Edward A. Berry <ber...@upstate.edu
<mailto:ber...@upstate.edu>> wrote:
Thanks- that works!
pdb-redo/tools/cif2cif in.cif out.cif
eab
On 03/13/2018 05:47 PM, Robbie Joosten wrote:
Hi Ed,
The pdb-redo program cif2cif does that. I implemented this feature
because there was no obvious CCP4 program that did this. You have to have your
data in mmCIF format though.
Cheers,
Robbie
Sent from my Windows 10 phone
-
-
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>>
on behalf of Edward A. Berry <ber...@upstate.edu <mailto:ber...@upstate.edu>>
*Sent:* Tuesday, March 13, 2018 10:25:25 PM
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* [ccp4bb] How to get Imean/SIGImean from separated anomalous
data?
I want to work with an mmcif file that has I+,sigI+,I-,SigI-;
in different columns for each reflection (no Imean).
cif2mtz gives those same columns in the output mtz, with or without
ANOMALOUS keyword.
cif2mtz and truncate seem to need the anomalous data as separate
reflections hkl and -h-k-l in order to calculate Imean or Fmean. What is the
best way to do this?
Thanks,
eab
Re: [ccp4bb] How to get Imean/SIGImean from separated anomalous data?
No problem with GUI2.. Eleanor On 13 March 2018 at 22:38, Edward A. Berry <ber...@upstate.edu> wrote: > Thanks- that works! > pdb-redo/tools/cif2cif in.cif out.cif > eab > > > On 03/13/2018 05:47 PM, Robbie Joosten wrote: > >> Hi Ed, >> >> The pdb-redo program cif2cif does that. I implemented this feature >> because there was no obvious CCP4 program that did this. You have to have >> your data in mmCIF format though. >> >> Cheers, >> >> Robbie >> >> Sent from my Windows 10 phone >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Edward >> A. Berry <ber...@upstate.edu> >> *Sent:* Tuesday, March 13, 2018 10:25:25 PM >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* [ccp4bb] How to get Imean/SIGImean from separated anomalous >> data? >> >> I want to work with an mmcif file that has I+,sigI+,I-,SigI-; >>in different columns for each reflection (no Imean). >> cif2mtz gives those same columns in the output mtz, with or without >> ANOMALOUS keyword. >> cif2mtz and truncate seem to need the anomalous data as separate >> reflections hkl and -h-k-l in order to calculate Imean or Fmean. What is >> the best way to do this? >> Thanks, >> eab >> >
Re: [ccp4bb] How to get Imean/SIGImean from separated anomalous data?
Thanks- that works! pdb-redo/tools/cif2cif in.cif out.cif eab On 03/13/2018 05:47 PM, Robbie Joosten wrote: Hi Ed, The pdb-redo program cif2cif does that. I implemented this feature because there was no obvious CCP4 program that did this. You have to have your data in mmCIF format though. Cheers, Robbie Sent from my Windows 10 phone -- *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Edward A. Berry <ber...@upstate.edu> *Sent:* Tuesday, March 13, 2018 10:25:25 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] How to get Imean/SIGImean from separated anomalous data? I want to work with an mmcif file that has I+,sigI+,I-,SigI-; in different columns for each reflection (no Imean). cif2mtz gives those same columns in the output mtz, with or without ANOMALOUS keyword. cif2mtz and truncate seem to need the anomalous data as separate reflections hkl and -h-k-l in order to calculate Imean or Fmean. What is the best way to do this? Thanks, eab
[ccp4bb] How to get Imean/SIGImean from separated anomalous data?
I want to work with an mmcif file that has I+,sigI+,I-,SigI-; in different columns for each reflection (no Imean). cif2mtz gives those same columns in the output mtz, with or without ANOMALOUS keyword. cif2mtz and truncate seem to need the anomalous data as separate reflections hkl and -h-k-l in order to calculate Imean or Fmean. What is the best way to do this? Thanks, eab
