Hi Joe,
You should also change the rlnDetectorPixelSize.
It may be easier to use relion_image_handler to rescale the map. It will
no longer be on the correct greyscale though.
HTH,
Sjors
PS: all this will be much easier in relion-2.0....
On 06/08/2016 10:25 PM, Wang, Joe wrote:
> Hi Sjors,
>
> I am trying to do the same thing. Instead of using other software to produce a magnified map, could I use relion_reconstruct and the data.star file to produce the magnified model? I tried to run it, but the result looks weird. Though I just realized that I didn't modified "rlnOriginOffsetsX/Y", is there any other reason that I may not be able to do so?
>
> Kindly,
> Joe
> --
> Joseph Che-Yen Wang, Ph.D.
> Staff Scientist
> Electron Microscopy Center
> Simon Hall 047D, 212 S. Hawthorne Drive
> Indiana University, Bloomington, IN 47405
> Phone +1-812-855-4963
> http://iubemcenter.indiana.edu/contact.html
>
> ________________________________________
> From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> on behalf of Sjors Scheres <[log in to unmask]>
> Sent: Wednesday, June 8, 2016 5:13 PM
> To: [log in to unmask]
> Subject: Re: [ccpem] Continue refining from bin 2 to bin 1 data
>
> Hi Huy,
> bin1 will indeed be faster than bin2...
> You could provide a upscaled reference at higher resolution, and a
> data.star file with the correctly rescaled rlnDtectorPixelSize, as well as
> rlnOriginOffsetsX/Y. Details have been discussed on this list. If you do,
> you can then start the refinement already from local angular searches.
> That should speed up things.
> Remember that rescaling does not need to be an integer factor. Any even
> box-size will do, so you could also try for example a box of 400x400.
> HTH,
> Sjors
>
>> Dear list,
>>
>> Anyone has any recommendation for routine going from bin 2 to bin 1
>> dataset? My workstation has only 128GB RAM and my box size is 512 x 512
>> unbinned. Using bin2 dataset (256 x 256), I already hit Nyquist frequency
>> resolution. Therefore, I need to go to unbinned dataset. From Relion FAQ,
>> it says that using bin1 will not increase the processing time. However,
>> the
>> refinement is going so slow and crash a lot of time due to lack of RAM.
>>
>> Is there anyway to continue the refinement of unbinned without going
>> through all the iteration from 60A to high res? Can I refine from the last
>> iteration of the bin 2 data further?
>>
>> I saw that it seems like I can modify the optimiser.star file as the
>> starting point for bin1 data set. Is this recommended to do so?
>>
>> Best,
>> Huy
>>
>
> --
> Sjors Scheres
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue, Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
> tel: +44 (0)1223 267061
> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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