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Re: [scipion-users] Masking issue -- 10x difference
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From: Dmitry S. <Sem...@gm...> - 2020-12-10 15:15:05
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Dear Grigory, Yes indeed it worked. Thank you! I still would like to understand why the recommended settings that are described in the Help for te protocol run: ProtRelionCreateMask do not work? As you see in this Help the 15-20 angstrom lowpass filter may work as well. Please see my test image below. Sincerely, Dmitry > On 10. Dec 2020, at 14:39, Grigory Sharov <sha...@gm...> wrote: > > 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 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Thu, Dec 10, 2020 at 10:53 AM Dmitry Semchonok <Sem...@gm... <mailto: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... <mailto:sha...@gm...>> wrote: >> >> I'll check this, thanks >> >> On Thu, Dec 10, 2020, 10:48 Dmitry Semchonok <Sem...@gm... <mailto: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... <mailto: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... <mailto: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... <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users <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> > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
