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Re: [scipion-users] phase shift data in "analyze results" gui ?
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From: Jonathan R. <re...@gm...> - 2018-04-14 14:15:31
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Thank you all for your help. We have just installed the development version (1.2) and it shows the phase shifts just as you say. This is a very helpful interface you have built. Best wishes, Jonathan On Sat, Apr 14, 2018 at 3:57 AM, Carlos Oscar Sorzano <co...@cn...> wrote: > Thank you, Gregory, for the clarification. > > On 14/04/2018 10:46, Gregory Sharov wrote: > > Hello, Jonathan > > As Pablo mentioned earlier, phase shift from gctf was incorrectly parsed > in many cases from output files in version 1.1, in 1.2 this should be > fixed now. Carlos is referring to phase shift calculation by xmipp, which > is not available yet. > > On Sat, Apr 14, 2018, 09:18 Carlos Oscar Sorzano <co...@cn...> wrote: > >> Dear Jonathan, >> >> phase shift was not calculated in v1.1, it has been added in the >> development branch, and it will be present in next release. >> >> Kind regards, Carlos Oscar >> >> On 13/04/2018 0:59, Jonathan Remis wrote: >> >> >> Hello, >> >> I am using SCIPION v1.1 and want to use a streaming data pipeline to give >> me a live readout of phase shifts as I collect images using gctf. Unlike >> most of the other information determined in the CTF estimation I don't see >> any columns for phase shift. I do see the values in >> >> */Runs/xxx_ProtGctf/extra/micrograph_name/ctfEstimation.txt * >> >> Perhaps there is a way to extract this data from the file but the format >> of the file doesn't allow me to grep it, or at least I don't know how to do >> this. >> >> If I am overlooking something or if you know of a way I could more easily >> get this information it would be quite useful. >> >> >> Thanks for your help< >> Jonathan >> >> >> -- >> >> ------------------------------ >> >> *JONATHAN REMIS* >> >> CryoEM Facilities Manager >> >> >> Northwestern University >> >> Department of Molecular Biosciences >> >> >> mailing address >> >> 2205 Tech Drive >> >> Hogan 2-100 >> >> Evanston, IL 60208-3500 >> >> USA >> >> >> *OFFICE* +1-847-491-7813 >> >> *EMAIL * jon...@no... <jon...@ab...> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=rZ6_ccPmCW2ygPRjtV6nCumy4R651ccxCN7scpmddvc&e=> >> >> >> >> _______________________________________________ >> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=WPo_z-oRa0Edn9oBkPY0haFyZXBVy35uvWJZMozqMJA&e=> >> >> >> -- >> ------------------------------------------------------------------------ >> Carlos Oscar Sánchez Sorzano e-mail: co...@cn... >> Biocomputing unit http://i2pc.es/coss <https://urldefense.proofpoint.com/v2/url?u=http-3A__i2pc.es_coss&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=ttaI9AfvlwszvKSNNMKdJFsXZNd6ygBzf4-kSgcF6Bw&e=> >> National Center of Biotechnology (CSIC) >> c/Darwin, 3 >> Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 >> 28049 MADRID (SPAIN) Fax: 34-91-585 4506 >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=rZ6_ccPmCW2ygPRjtV6nCumy4R651ccxCN7scpmddvc&e=> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=WPo_z-oRa0Edn9oBkPY0haFyZXBVy35uvWJZMozqMJA&e=> >> > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=rZ6_ccPmCW2ygPRjtV6nCumy4R651ccxCN7scpmddvc&e=> > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=WPo_z-oRa0Edn9oBkPY0haFyZXBVy35uvWJZMozqMJA&e=> > > > -- > ------------------------------------------------------------------------ > Carlos Oscar Sánchez Sorzano e-mail: co...@cn... > Biocomputing unit http://i2pc.es/coss <https://urldefense.proofpoint.com/v2/url?u=http-3A__i2pc.es_coss&d=DwMDaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=PKouI9iuvAtcTalJlP6CmPmHJABzL5IGqm7dbafbFe0&s=ttaI9AfvlwszvKSNNMKdJFsXZNd6ygBzf4-kSgcF6Bw&e=> > National Center of Biotechnology (CSIC) > c/Darwin, 3 > Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 > 28049 MADRID (SPAIN) Fax: 34-91-585 4506 > ------------------------------------------------------------------------ > > |
