 |
 |
Hi Tat, The simplest way is to use Chimera to manually fit two maps by adjusting the pixel size of one while keep the other(ref.) unchanged. Note the update of CCC each time after you re-fit the pair of maps. Alternatively there are many programs that can calculate the CCC between two maps(I can share you mine), you can write a script to get the maximum CCC against scaling factors. Best wishes, Kai > Hi Kai, > > Thank a lot, this is really useful. > I have been gauging the "correct" pixel size by comparing the CC between > model and map, which presume that the existence of a "correct" model. So > my question is: what is the best way to determine the correct pixel size > when dealing with a novel map without any model? > Thanks again. > > Tat > ________________________________ > From: Collaborative Computational Project in Electron cryo-Microscopy > [[log in to unmask]] on behalf of kzhang [[log in to unmask]] > Sent: Wednesday, February 17, 2016 11:37 AM > To: [log in to unmask] > Subject: Re: [ccpem] Strategy on combining datasets > > Dear Arko, > > Find the attached for optimized strategy for combinding datasets. > This PPT was from a talk last year in LMB about CTF (for more inforamtion > and details, email me personally). > The strategy has been proved to work very well in several case of my own > and my colleagues. > > Note the following facts: > 1) You don't actually know the precise pixel size for each magnifcation > just from the readout of microscope. Even after calibration using standard > sample like graphite black, this is usually far from the requirement for > accurate dataset combination. > 2) The CTF and precise scaling factor is the critical factor to limit the > final resolution; > 3) Optimizing the box sizes would also help a lot for high resolution; > 4) The higher defocus the stricter criterion you should use. > > Best wishes > Kai > > ________________________________ > 发件人：Arka Chakraborty <[log in to unmask]> > 发送时间：2016-02-16 11:52 > 主题：Re: [ccpem] Strategy on combining datasets > 收件人："CCPEM"<[log in to unmask]> > 抄送： > > Dear Dr. Xiaodi, Dear Dr. Sjors, > > Thanks a lot for your inputs. As I have already done 3D classification for > one of the data sets I will follow Dr. Sjors's suggestion on aligning and > summing the half maps. I have a related question regarding > relion_image_handler. For resetting the box size for the reference for 3D > classification the new_box input needs to be in pixels. However the 3d > classification seems only to work when I prepare the reference with the > same numerical value as is stated in general inputs tab (which is however > in angstroms)..am I missing something here?..could you please comment? > > Thanks a lot, > > Regards, > > Arko > > On Tue, Feb 16, 2016 at 10:09 AM, Sjors Scheres > <[log in to unmask]<mailto:[log in to unmask]>> wrote: > Dear Arko, > You could rescale one data set to a pixel size as similar as possible as > the other one, and process the 2 data sets together. In that case be > alert > of classification into the original 2 data sets. > Alternatively, you could rescale and align the 2 unfil.mrc half-maps of > one data set on top of the half-maps from the other data set. Then, add > the half1 maps from both data sets together, as well as the half2 maps. > You can then perform postprocessing on the 2 summed half-maps to get your > combined map. > HTH, > Sjors > >> Dear CCPEM-ers, >> >> I would like to have some advice on the optimal way to combine two data >> sets for single particle reconstruction in relion-should that be >> performed >> at the stage of 3D classification (averaging 3D classes?) or after 3D >> refinement (averaging the 3D volumes obtained in each case)? (in the >> later >> case how would one go about calculating 'gold standard' FSC?..Would it >> be >> advisable to average the final volumes obtained by separate processing >> of >> the two datasets?..Is there a possibility of combining the data sets >> from >> scratch? (how to bring the images onto a common scale in that case)?. >> Any >> inputs and/or practical advices will be greatly appreciated. >> >> Best regards, >> >> Arko >> >> -- >> *Arka Chakraborty* >> *ibmb (Institut de Biologia Molecular de Barcelona)* >> *BARCELONA, SPAIN* >> > > > -- > Sjors Scheres > MRC Laboratory of Molecular Biology > Francis Crick Avenue, Cambridge Biomedical Campus > Cambridge CB2 0QH, U.K. > tel: +44 (0)1223 267061<tel:%2B44%20%280%291223%20267061> > http://www2.mrc-lmb.cam.ac.uk/groups/scheres<https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.mrc-2Dlmb.cam.ac.uk_groups_scheres&d=AwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=qT2ELyXV7cIjnYr4ZwzxwxJqTwi_l5n0PWGWivC_fRs&m=siExkny0X_x76FTH6nV1PKtQVIB3zUajZzP6wlcPzhQ&s=bSWtk_AyS0g1UU7DdfSiO_Tfa6DymWnjFS3Vm629_c8&e=> > > > > > -- > Arka Chakraborty > ibmb (Institut de Biologia Molecular de Barcelona) > BARCELONA, SPAIN >