Re: [ccp4bb] [xds] how to specify measuring angle
On 2020-10-09 01:59, Dirk Kostrewa wrote: Dear Doo Nam Kim, On 09.10.20 08:43, Doo Nam Kim wrote: Since I don't know correct value of OSCILLATION_RANGE, I just changed to the example value (0.1) from (0.89976, I know it is not a positive multiple of 0.0001, but worked for ketone data). without knowing the correct value for the OSCILLATION_RANGE, data processing might run through but produces non-sense results, independent of the data processing program you use. So, it is absolutely important to know the correct value for the oscillation range per frame. For these data, the oscillation range should be 0.37 degrees, because the rotation rate is 0.09 degrees per second (as per SBGrid reprocessing instructions) and the time between successive frames is ~4.1 s (as determined by tvips2smv). I just checked, and this is indeed what's in OSC_RANGE header item, assuming you actually used tvips2smv to make the SMV files. // Cheers; Johan 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] [xds] how to specify measuring angle
Hi Doo Nam Kim, If you do not know your OSCILLATION_RANGE, a good guess would be to take your collection angle range (-60 to +60 or 120 degrees) and divide that by the number of frames. Best, Jessica On Fri, Oct 9, 2020 at 2:00 AM Dirk Kostrewa < dirk.kostr...@lrz.uni-muenchen.de> wrote: > Dear Doo Nam Kim, > > On 09.10.20 08:43, Doo Nam Kim wrote: > > Since I don't know correct value of OSCILLATION_RANGE, I just changed to > the example value (0.1) from (0.89976, I know it is not a positive > multiple of 0.0001, but worked for ketone data). > > without knowing the correct value for the OSCILLATION_RANGE, data > processing might run through but produces non-sense results, independent > of the data processing program you use. So, it is absolutely important > to know the correct value for the oscillation range per frame. > > Cheers, > > Dirk. > > -- > > *** > Dirk Kostrewa > Gene Center Munich > Department of Biochemistry, AG Hopfner > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > D-81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax:+49-89-2180-76998 > E-mail: dirk.kostr...@lmu.de > WWW:www.genzentrum.lmu.de > strubio.userweb.mwn.de > *** > > > > 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/ > -- Jessica Bruhn, Ph.D Principal Scientist NanoImaging Services, Inc. 4940 Carroll Canyon Road, Suite 115 San Diego, CA 92121 Phone #: (888) 675-8261 www.nanoimagingservices.com 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] [xds] how to specify measuring angle
Dear Doo Nam Kim, On 09.10.20 08:43, Doo Nam Kim wrote: Since I don't know correct value of OSCILLATION_RANGE, I just changed to the example value (0.1) from (0.89976, I know it is not a positive multiple of 0.0001, but worked for ketone data). without knowing the correct value for the OSCILLATION_RANGE, data processing might run through but produces non-sense results, independent of the data processing program you use. So, it is absolutely important to know the correct value for the oscillation range per frame. Cheers, Dirk. -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de WWW:www.genzentrum.lmu.de strubio.userweb.mwn.de *** 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] [xds] how to specify measuring angle
Dear Doo Nam Kim, actually the results of XDS processing are deterministic for all practical purposes (to be nitpicking, the multi-processor version xds_par may result in slighly different output each time it is run, because for a few calculations the order of operations is influenced by the operating system's scheduler, but this only typically affects the last digit and is of no practical importance). XDS needs to know the starting and end angle of each frame. It calculates these values internally, from STARTING_ANGLE and OSCILLATION_RANGE and the frame number (you specify the frames to process with DATA_RANGE for INTEGRATE, and with SPOT_RANGE for COLSPOT and IDXREF). If you don't specify STARTING_ANGLE, it will use 0 as the default. This does not affect the success of indexing, nor the data quality. There is no corresponding ENDING_ANGLE, because - as I said - the ENDING_ANGLE is anyway calculated internally; it is the end angle of the last frame. Concerning completeness: if your DATA_RANGE is specified correctly, AND the indexing succeeds, AND the space group is found (or given) correctly, then I see no reason why the completeness should not result in 60% for you, if someone else got 60%. Apart from http://xds.mpimf-heidelberg.mpg.de, there is documentation and examples in XDSwiki at https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Main_page Hope this helps, Kay On Fri, 9 Oct 2020 07:43:22 +0100, Doo Nam Kim wrote: >Thank you Tim and Kay. > > > >"the indexing procedure is independent of the starting angle of the first >frame." >--> I see, since XDS does indexing, I think that XDS is independent of the >starting angle of the first frame > > >"Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree >per frame during data collection?" > >--> As I see >http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#OSCILLATION_RANGE= > >OSCILLATION_RANGE= ! (not OSCILLATION_WIDTH!) >appears to designate 1 value, rather than 2 values (like min and max, e.g. >-60, 60). > >Since I don't know correct value of OSCILLATION_RANGE, I just changed to the >example value (0.1) from (0.89976, I know it is not a positive multiple of >0.0001, but worked for ketone data). > >Then, xds ran without error. > >Then, according to recommendtion, I changed from >JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT >to >JOB= DEFPIX INTEGRATE CORRECT > >and ran again. > >This time, it generated CORRECT.LP, but I see COMPLETENESS is only ~6%, while >my predecessor achieved ~60% > >I think that results of XDS are somehow random (not 100% deterministic). But I >didn't expect this big difference of COMPLETENESS (6% vs 60%). > >I think that I still entered a wrong option value somewhere in my XDS.INP. > >I think that I need to use well documented (with respect to needed xds.INP >parameters) microED dataset but I can't download from >https://cryoem.ucla.edu/MicroED > > > >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/ 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] [xds] how to specify measuring angle
Once I turned off my vpn, I could download from https://data.sbgrid.org/dataset/222/ Thank you for your help. 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] [xds] how to specify measuring angle
Thank you Tim and Kay. "the indexing procedure is independent of the starting angle of the first frame." --> I see, since XDS does indexing, I think that XDS is independent of the starting angle of the first frame "Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree per frame during data collection?" --> As I see http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#OSCILLATION_RANGE= OSCILLATION_RANGE= ! (not OSCILLATION_WIDTH!) appears to designate 1 value, rather than 2 values (like min and max, e.g. -60, 60). Since I don't know correct value of OSCILLATION_RANGE, I just changed to the example value (0.1) from (0.89976, I know it is not a positive multiple of 0.0001, but worked for ketone data). Then, xds ran without error. Then, according to recommendtion, I changed from JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT to JOB= DEFPIX INTEGRATE CORRECT and ran again. This time, it generated CORRECT.LP, but I see COMPLETENESS is only ~6%, while my predecessor achieved ~60% I think that results of XDS are somehow random (not 100% deterministic). But I didn't expect this big difference of COMPLETENESS (6% vs 60%). I think that I still entered a wrong option value somewhere in my XDS.INP. I think that I need to use well documented (with respect to needed xds.INP parameters) microED dataset but I can't download from https://cryoem.ucla.edu/MicroED 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] [xds] how to specify measuring angle
I agree with Tim that Doo Nam Kim's question appears to be directed towards the rotation per frame, which is specified in XDS.INP using OSCILLATION_RANGE= ! (not OSCILLATION_WIDTH!) please see the documentation at http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#OSCILLATION_RANGE= best, Kay On Thu, 8 Oct 2020 11:04:21 +0200, Tim Gruene wrote: >Dear Doo Nam Kim, > >the indexing procedure is independent of the starting angle of the >first frame. > >Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree >per frame during data collection? > >Best regards, >Tim > >On Thu, 8 Oct 2020 09:28:07 +0100 >Doo Nam Kim <4e720d49e642-dmarc-requ...@jiscmail.ac.uk> wrote: > >> I think that my microED data was measured with -60 to 60 rotation >> angle. >> >> However, >> STARTING_ANGLE= -60. >> in my XDS.INP >> >> resulted in >> ... >> # COORDINATES OF REC. BASIS VECTORREDUCED CELL INDICES >> >> 1 0.0020349 0.0108237 0.0096964 1.00 -0.00 -0.00 >> 2 -0.0056895-0.0002762 0.0015024 0.001.00 -0.00 >> 3 0.0011313-0.0034716 0.0036457 0.00 -0.001.00 >> >> >> * REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1 >> * !!! ERROR IN REFINE !!! RETURN CODE IS IER= 0 >> >> I assume that rotation angle should be specified in XDS.INP. >> >> Anyone knows how to specify measuring angle in XDS.INP? >> >> If there's no such option in XDS.INP, please let me know as well. >> Then, my other part of XDS.INP should be corrected. >> >> Thank you >> >> >> >> 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/ > > > >-- >-- >Tim Gruene >Head of the Centre for X-ray Structure Analysis >Faculty of Chemistry >University of Vienna > >Phone: +43-1-4277-70202 > >GPG Key ID = A46BEE1A > > > >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/ > 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] [xds] how to specify measuring angle
Dear Doo Nam Kim, the indexing procedure is independent of the starting angle of the first frame. Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree per frame during data collection? Best regards, Tim On Thu, 8 Oct 2020 09:28:07 +0100 Doo Nam Kim <4e720d49e642-dmarc-requ...@jiscmail.ac.uk> wrote: > I think that my microED data was measured with -60 to 60 rotation > angle. > > However, > STARTING_ANGLE= -60. > in my XDS.INP > > resulted in > ... > # COORDINATES OF REC. BASIS VECTORREDUCED CELL INDICES > > 1 0.0020349 0.0108237 0.0096964 1.00 -0.00 -0.00 > 2 -0.0056895-0.0002762 0.0015024 0.001.00 -0.00 > 3 0.0011313-0.0034716 0.0036457 0.00 -0.001.00 > > > * REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1 > * !!! ERROR IN REFINE !!! RETURN CODE IS IER= 0 > > I assume that rotation angle should be specified in XDS.INP. > > Anyone knows how to specify measuring angle in XDS.INP? > > If there's no such option in XDS.INP, please let me know as well. > Then, my other part of XDS.INP should be corrected. > > Thank you > > > > 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/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A 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/ pgpz9OxPGhw8u.pgp Description: OpenPGP digital signature
[ccp4bb] [xds] how to specify measuring angle
I think that my microED data was measured with -60 to 60 rotation angle. However, STARTING_ANGLE= -60. in my XDS.INP resulted in ... # COORDINATES OF REC. BASIS VECTORREDUCED CELL INDICES 1 0.0020349 0.0108237 0.0096964 1.00 -0.00 -0.00 2 -0.0056895-0.0002762 0.0015024 0.001.00 -0.00 3 0.0011313-0.0034716 0.0036457 0.00 -0.001.00 * REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1 * !!! ERROR IN REFINE !!! RETURN CODE IS IER= 0 I assume that rotation angle should be specified in XDS.INP. Anyone knows how to specify measuring angle in XDS.INP? If there's no such option in XDS.INP, please let me know as well. Then, my other part of XDS.INP should be corrected. Thank you 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/
