Hi Cristina,

In the next version of relion, padding will be switched off by default in
3D refinements and classifications. (It will become an option on the GUI.)
Non-padded reconstructions will also need larger boxes than the particle
'almost touching the box' to prevent artifacts folding back into the
corners.

I think when reviewing the quality of the map should be the key. There are
perhaps always things that could have potentially been done better, but
good enough is good enough. Sometimes figures are not the best to assess
map quality, and submitting the map for review too can help. But that's a
completely different discussion
that has surfaced in the past. :-)

HTH,
Sjors


> Hi Sjors,
> Yes my observation are without the argument. Good point!
> How would you and the community asses the fact that most use too small box
> sizes. In principle it is not incorrect as it will only affect
> high-resolution of highly defocused particles and if your map looks fine
> that it is kind of ok I guess. But it will affect it stronger at the
> periphery of the particles than at the center. Is this something we should
> address stronger for example during review or from the deposition site?
> And sure I can assess the box size from the EMDB but I think this should
> be a must-have value to include in any cryo-EM table of manuscripts which
> is currently not in the default tables provided at least by high-impact
> journals.
> Cristina
>
>
>> On 20 Mar 2018, at 6:33 PM, Sjors Scheres <[log in to unmask]>
>> wrote:
>>
>> Hi Cristina,
>>
>> The observations about CTF effects spreading signal outside the box are
>> correct and should be heeded.
>>
>> About your observations: smaller box sizes have relatively more signal
>> in the box and less noise. Therefore, if you don't use
>> --solvent_correct_fsc, then the unmasked FSC curve that is used inside
>> relion_refine will underestimate the signal more for larger boxes. This
>> can then lead to less accurate alignments and thus lower resolutions.
>> This was one of the reasons to introduce --solvent_correct_fsc, which
>> will basically do a post-processing like correction of the FSC curve
>> during refinement to take into account that the signal only lives in a
>> small part of the box. Could ti be your observations are without this
>> argument?
>>
>> HTH,
>>
>> Sjors
>>
>>
>>
>> On 03/20/2018 04:31 PM, Cristina Paulino wrote:
>>> Dear all,
>>> I am actually very glad that this topic was brought up as I have been
>>> puzzled for a while looking at the box sizes of published structures.
>>> My impression is the the box sizes are decreasing per publication, and
>>> it became almost normal in my eyes to see box sizes where the
>>> particles almost touch the box edges. (Unfortunately more and more
>>> publications don’t specify the size of their box size in the material
>>> and methods nor in the cryo-EM table).
>>> Me and my group have been playing around with this for a while and I
>>> always was more on the big-box-size-side, exactly with the intention
>>> of including all delocalised high resolution information.
>>> However, I can confirm that the resolution given from an FSC plot
>>> often improves quite a bit when using a smaller box size. And this
>>> intrigues me even more. I thought it might be because a smaller box
>>> size masks more noise out and this might be of greater benefit than
>>> including high-resolution of highly defocused particles in the
>>> dataset. But shouldn't the masking out of noise be covered by the
>>> final mask in the post-processing step? And again I am puzzled.
>>> Even if the FSC resolution gets better, and the map looks ok one clear
>>> consequence of going to a final smaller box size is that while the
>>> center of your particle will be less affected, you will exclude more
>>> high-resolution information for protein feature at the edges of your
>>> particle as their delocalised information will be further away. This
>>> also explains (partially) the typical appearance of local resolution
>>> maps with a high-resolved protein-core and a less resolved
>>> protein-edge.
>>> So how should we proceed here? I am afraid most people would always go
>>> for the approach that gives the better FSC resolution, even though
>>> this might sometimes not be the best approach to treat your data.
>>>
>>> Best,
>>> Cristina
>>>
>>>
>>>
>>>
>>>> On 20 Mar 2018, at 4:48 PM, Leonid Sazanov <[log in to unmask]
>>>> <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
>>>>
>>>> Hi, this is from Rosenthal and Henderson JMB 2003 paper, page 726:
>>>>
>>>> Minimal box size to achieve resolution d, for particle with diameter
>>>> D, with defocus dF and wavelength L (~0.02 for 300 kV):
>>>>
>>>> Box = D + ( 2 x L x dF / d ),
>>>>
>>>> i.e. for particle 200 A, max defocus in dataset  2.0 um and to
>>>> achieve resol 3.5 A => 200 + ~230 A = 430 A box.
>>>>
>>>> Best,
>>>>
>>>> Leonid
>>>>
>>>> Prof. Leonid Sazanov
>>>> IST Austria
>>>> Am Campus 1
>>>> A-3400 Klosterneuburg
>>>> Austria
>>>>
>>>> Phone: +43 2243 9000 3026
>>>> E-mail: [log in to unmask] <mailto:[log in to unmask]>
>>>> On 20/03/18 12:41, Teige Matthews-Palmer wrote:
>>>>> Dear Bum-Han,
>>>>>
>>>>> I agree, I think the background circle is just for normalisation. I
>>>>> never tried changing the default - do many people?
>>>>> So to answer Joshua’s question making the circle smaller
>>>>> shouldn’t
>>>>> help with the issue of duplicates. There is also the diameter of the
>>>>> circle/spherical mask during classification as you say, but I
>>>>> /think/ the mask isn’t fixed to the particle image during
>>>>> translation so again it won’t help. (Please correct me if wrong!)
>>>>>
>>>>> As for box-size, the previous discussion
>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCPEM;2b838c96.1802
>>>>> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCPEM;2b838c96.1802>
>>>>> highlighted
>>>>> that the ability to make a larger translational search in a large
>>>>> box is a *disadvantage* because (especially poor autopicking) the
>>>>> boxes contain more than one particle and the search creates
>>>>> duplicate particles in your dataset. Undetected duplicate particles
>>>>> erroneously increase the FSC between random half-sets.
>>>>> The advantage of a large box is that you can be confident that the
>>>>> box contains all the high-spatial-frequency information of your
>>>>> particle (that is spread out in real-space by the
>>>>> point-spread-function); so when you perform CTF correction, all the
>>>>> high resolution info is available.
>>>>>
>>>>> I think the ideal box-size is a balance of: 1) large enough to
>>>>> contain all the PSF convolution of your particle; but 2) small
>>>>> enough that your dataset is practical to compute classifications.
>>>>> (So downsampling is helpful.)
>>>>> Does anyone know of a paper or webpage about estimating the size of
>>>>> the PSF to help make an informed choice when extracting a larger
>>>>> box? Bad picking and greater underfocus would need larger boxes.
>>>>>
>>>>> Personally, I don’t think that creating duplicate particles should
>>>>> be a driving reason to decrease box size; it’s surely better to
>>>>> check for duplicates as many have suggested. (P.S. scipion’s
>>>>> consensus pick might have the underlying ability I couldn’t get it
>>>>> to remove duplicate coordinates from a single coordinate set.)
>>>>>
>>>>> All the best, and grateful for any corrections,
>>>>> Teige
>>>>>
>>>>> 1)
>>>>> https://www.youtube.com/watch?v=GYDLhg49UQA&index=27&list=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8-
>>>>> <https://www.youtube.com/watch?v=GYDLhg49UQA&index=27&list=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8->
>>>>> /The
>>>>> micrographs are an image of the specimen, convoluted by PSF, and
>>>>> since the contrast-transfer-function (CTF) is the Fourier transform
>>>>> of the PSF, when we CTF correct in Fourier space we hope to
>>>>> deconvolve the image from its PSF. If some of the spread-out signal
>>>>> of our particle is outside the box, then the CTF correction won’t
>>>>> restore the highest (most spread) spatial frequencies./
>>>>> /
>>>>> /
>>>>> /2) Information to help predict RAM usage for a given boxsize &
>>>>> N:
>>>>> https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Calculate_2D_class_averages/
>>>>> <https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Calculate_2D_class_averages/>
>>>>> /
>>>>> /
>>>>>> On 19 Mar 2018, at 15:34, 류범한 <[log in to unmask]
>>>>>> <mailto:[log in to unmask]>
>>>>>> <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
>>>>>>
>>>>>> Dear Sjors,
>>>>>>
>>>>>> I also wonder the question Joshua brought up.
>>>>>>
>>>>>> As I have understood (I am not sure I think this matter in right
>>>>>> way), setting background diameter circle is likely to define the
>>>>>> reference region for normalization, which makes signals seemingly
>>>>>> outstanding (?) and therefore contributes to find meaningful
>>>>>> signals or particles easier against background noise. In other
>>>>>> words, setting background diameter should be related to
>>>>>> background-quality (or SNR). When you play with low SNR or dirty
>>>>>> background micrographs, I think that adjusting background diameter
>>>>>> may give us better results.
>>>>>>
>>>>>> Meanwhile, I am not sure why the bigger box is advantageous (refer
>>>>>> to Ch.6 in Methods in Enzymology, Volume 579).
>>>>>> As I think, if the bigger box size can be better than the smaller
>>>>>> one, bigger box (two fold of the largest particle dimension is
>>>>>> suggested) should guarantee more possibility to find and align
>>>>>> signals corresponding to a particle in the box (=conservative
>>>>>> TRANSLATION?), especially when the center of mass is hard to be
>>>>>> defined due to improper autopicking or noisy micrographs.
>>>>>>
>>>>>> All these are just my views. I am not sure how much my ideas are
>>>>>> close to the fact. Am I thinking in right way to the above?
>>>>>>
>>>>>> Any comment is welcomed !
>>>>>>
>>>>>>
>>>>>> Best,
>>>>>> Han
>>>>>> *
>>>>>> *
>>>>>> *
>>>>>> *
>>>>>> *Bum Han Ryu*
>>>>>>
>>>>>> Postdoctoral Researcher
>>>>>> Korea Basic Science Institute (KBSI)
>>>>>> 161 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-si
>>>>>> Chungcheongbuk-do, Republic of Korea
>>>>>>
>>>>>> Office) 043-240-5329
>>>>>>
>>>>>> <한국기초과학지원연구원CI_영문가로형
>>>>>> (축소).jpg>
>>>>>>
>>>>>>> 2018. 3. 3. 오전 7:02, Joshua Lobo <[log in to unmask]
>>>>>>> <mailto:[log in to unmask]>
>>>>>>> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
>>>>>>> 작성:
>>>>>>>
>>>>>>> Hi CCPEM
>>>>>>>
>>>>>>> I'm sorry to bring this discussion up again as in the link
>>>>>>>
>>>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCPEM;2b838c96.1802
>>>>>>>
>>>>>>> and yes, I definitely wholeheartedly agree with Bjorn's excellent
>>>>>>> points.And I also agree that the ideal case would be extracting a
>>>>>>> single particle per box. But in a sample where there are crowded
>>>>>>> particles would changing the diameter of the background circle
>>>>>>> during extraction be a better way than extracting with a bigger
>>>>>>> box and masking out only the single particle of interest. in the
>>>>>>> 2D classification step?
>>>>>>>
>>>>>>>
>>>>>>> Sincerely
>>>>>>> Joshua Lobo
>>>>>>
>>>>>
>>>>> The Francis Crick Institute Limited is a registered charity in
>>>>> England and Wales no. 1140062 and a company registered in England
>>>>> and Wales no. 06885462, with its registered office at 1 Midland Road
>>>>> London NW1 1AT
>>>>>
>>>>
>>>
>>
>> --
>> 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
>> <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