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Re: [scipion-users] Masking issue -- 10x difference
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From: Grigory S. <sha...@gm...> - 2020-12-10 13:39:48
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Hi, I've checked this and as I said before your comparison is wrong. Set in relion lowpass to -1, extend and soft edge to 0 and then the same threshold as in xmipp will give you (almost) the same volume. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Dec 10, 2020 at 10:53 AM Dmitry Semchonok <Sem...@gm...> wrote: > I guess it happens not often, but I noticed that happening more ofter > after the bayesian polishing. > > The log shows the same values as I set in. > > Please let me know in case you want see the problem on our server directly > (if it can help somehow). > > > Sincerely, > Dmitry > > > > > On 10. Dec 2020, at 11:51, Grigory Sharov <sha...@gm...> > wrote: > > I'll check this, thanks > > On Thu, Dec 10, 2020, 10:48 Dmitry Semchonok <Sem...@gm...> wrote: > >> Dear Carlos Oscar and Grigory, >> >> Thank you for your answers. >> >> The following image illustrates the problem. >> >> 1. Thank you Carlos Oscar — on the image below I compared the Xmipp >> masking and is works as it should based on the correct threshold. >> 2. Thank you Grigory — no the binning value seems to be ok. >> >> >> Sincerely, >> Dmitry >> >> >> >> >> >> >> >> >> >> >> >> >> On 10. Dec 2020, at 11:32, Grigory Sharov <sha...@gm...> >> wrote: >> >> Hi, >> >> You can check the output log for the protocol to see the executed relion >> command. I think you have lowpass filtering enabled so the threshold you >> choose must be selected on a filtered volume. >> >> On Thu, Dec 10, 2020, 08:47 Dmitry Semchonok <Sem...@gm...> wrote: >> >>> Dear colleagues, >>> >>> >>> It may be the bug of issue happening after the particle polishing with >>> the relion masking 3D protocol. >>> >>> >>> It seems that it has a 10x times issue. >>> >>> So, adjusting the volume threshold in chimera (for 3D mask protocol and >>> then postprocessing) till no extra noise is appeared we get the value for >>> ex. 0.00658. But if you then put this value to the relion 3D mask protocol >>> you get completely dark images. At the same time if you set the threshold >>> value 0.000658 you get the fine mask. >>> >>> >>> I am not sure what causes that but I noticed that behaviour happening >>> sometimes after the execution of the Bayesian polishing. >>> >>> >>> Sincerely, >>> >>> Dmitry >>> >>> >>> P.s. it will be great to have unbiased protocol for masking >>> Or is there any exist already? >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> <Screenshot 2020-12-10 at 11.40.39.png><Screenshot 2020-12-10 at > 11.40.39.png> > > > |
