In global refinement, this is handled automatically, and I do not believe there is a way to “force” finer angular samplings. In local refinement there is an option to choose the maximum angular sampling (by default 0.2deg).
There is no way to select based particles based on figure of merit (I guess you are thinking like Pmax in relion) in cryoSPARC, to my knowledge. You can select particles based on probability of belonging to a particular class, after 2D or 3D classification, using the Class Probability Filter job type.
How do I introduce an already computed moderate resolution density map as a starting model in the workflow of cryosparc.
I have the particles boxed out, class averaged, classes selected and particles extracted for reconstruction. At this point instead of using Ab-Initio reconstruction I want to use the pre-computed map as the starting mode and continue with the refinement.
How do I get the program (cryosparc) to read this precomputed map into its pipeline.
How can I get the extracted particles (in mrc format)
Not sure what you mean - are you asking how to export to read into relion? Or another program? It will depend on what you want to do with them (in terms of how best to export)
for point no. 2, yes, - how to read the particles in another program - like say BSOFT or EMAN2 etc. I want to do some pre-processing for starting the model refinement or generate a starting model using BSOFT or EMAN 2. Can I get the particle images (stacks) from each micrograph (after frame alignment and dose correction).
Also can I get particles ctf corrected before the reconstruction process ?
While carrying out class averaging for particles I encountered " illegal memory access was encountered". I do not find a solution to overcome this. Additionally this happened when I am trying to add another set of data to the existing one (which already provided a 3.4 Å resolution map).
Any feedback and a fix to the problem will be helpful.
@Andy Please can you add more details about the error:
cryoSPARC job type
where in the logs or interface the error was encountered, with additional lines of output for context
the current “physical” box size of the particle stacks and any job parameters that affect the job’s memory complexity (resolution, number of classes, particles, etc.)
hardware and software:
how the other dataset was added to the existing one, and how the datasets differ
The above issue also taken care of at present (BUT I will revisit it later to provide you more details). I have another problem.
I recently completely a helical reconstruction with resolution up to 3.6Å. Now I want to generate the whole 3.6Å map to a much larger length (it is a phage tail density map). I will need the asymmetric map (at 3.6Å) so that I can symmetrize it to generate a 1200Å long map (the map is ~256Å long). How to obtain the asymmetric map ?
Is there any alternate way to do it ?
I want to sort out heterogeneity based on the Pitch of the helix. I can generate maps for classifications from the asymmetric map, requested above. Following that How to I carry out the classification using the maps in cryosparc ?
I binned the images in BSOFT (or you can do it in any package like EMAN2) and then imported them in Cryosparc.
However if memory serves well, there should be an option in cryosparc, I can possibly reply you back tomorrow or day after tomorrow. Some one from cryosparc team can definitely reply you, sooner but you can try the ‘Fourier crop to box size’.
Depending on your stage of the workflow, “binning” can be accomplished in various job types.
For example, see this discussion about Patch Motion Correction.
Additionally, there are the Extract From Micrographs and Downsample Particles job types that can achieve a binning effect.
I’m running the Topaz Extract job, but it errored “out of memory”. I thought if I can bin the micrograph in a separate job, then do the Topaz extract, this error may cleared.
Hi @CleoShen - the defaults for topaz extract are quite memory hungry - you might try reducing the number of threads and processes, if you haven’t already.
Thank you for your reply.
I binned the micrographs by Patch Motion Cor Job, then the Topaz Extract works, but I would like to downsample more, such as bin8, bin16, but the CS Patch Motion Cor F-crop option only provides as many as bin4, if you know how can I downsample more in CS?
This shouldn’t be necessary to run Topaz, as Topaz downsamples on the fly. Have you tried adjusting the downsampling factor in Topaz? What settings are you using?