[3dem] [EXT] NaNs error in 3D variability job in cryoSPARC

[Sepideh Valimehr]

Hi Hamish,

Thanks for your reply. I got the volume from PDB file in chimera and then
used the resample command to align it with the volume from refinement job
then import the volume to cryoSPARC and made the mask in cryoSPARC. When I
check the mask from cryoSPARC with the map it looks fine.

Bests,
Sepideh

On Mon, Oct 26, 2020 at 9:52 AM Hamish Brown <hgbrown at unimelb.edu.au> wrote:

> Hi Sepideh,
>
> It sounds like something might be going wrong in the translation of the
> mask from Chimera to cryoSPARC and perhaps a volume outside the bounds of
> the object is being masked (though I would have thought this would have
> thrown an error before cryosparc progressed to eigenvalue analysis). Did
> you use the Chimera command "vop resample #1 onGrid #2", where #1 is your
> off-grid mask and #2 is your original structure, before exporting the mask
> from Chimera? See the section on mask creation in "
> https://urldefense.com/v3/__https://cryosparc.com/blog/local-refinement__;!!Mih3wA!UN6IqSqycqOAuSRvhqbCnT9blFrCENVqAa9v_u9nTssEI5tg0lpvBjDLIwj2T2JC0w$ ". As a check you can download
> the mask and input volume from the 3D variability job and input them into
> chimera before applying any translation or rotation to see if they line up
> as intended.
> cryoSPARC | Leading Cryo-EM Software Solutions
> <https://urldefense.com/v3/__https://cryosparc.com/blog/local-refinement__;!!Mih3wA!UN6IqSqycqOAuSRvhqbCnT9blFrCENVqAa9v_u9nTssEI5tg0lpvBjDLIwj2T2JC0w$ >
> cryoSPARC | Leading Cryo-EM Software Solutions. Local Refinement Beta in
> cryoSPARC v2 September 17, 2018 Ali Haydaroglu. With cryoSPARC v2.2, we are
> rolling out a beta version of a new set of tools to refine your dynamic and
> flexible structures down to atomic resolutions!For now, the Local
> Refinement toolkit includes Particle Subtraction and Local Refinement jobs
> that can be implemented in ...
> cryosparc.com
> Cheers,
>
> *Dr Hamish G Brown | Electron Cryo Microscopy Fellow*
>
> Advanced Microscopy Facility | Bio21 Molecular Science & Biotechnology
> Institute
>
> 30 Flemington Road, Parkville Victoria 3052
>
> *E: *hgbrown at unimelb.edu.au
>
> *T: *+61383440959 <hgbrown at unimelb.edu.au>
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> my respects to the Elders, past and present.*
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> ------------------------------
> *From:* 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Sepideh Valimehr <
> svalimehr at student.unimelb.edu.au>
> *Sent:* 21 October 2020 09:33
> *To:* 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
> *Subject:* [EXT] [3dem] NaNs error in 3D variability job in cryoSPARC
>
> * UoM notice: External email. Be cautious of links, attachments, or
> impersonation attempts *
> ------------------------------
> Dear all,
>
> I have NaNs error in 3D variability in cryoSPARC . I am trying to repeat
> the 3D variability analysis based on the recent paper of Key Lewis “Probing
> cooperativity of N-terminal domain orientations in the p97 molecular
> machine: synergy between NMR and cryo-EM. Rui Huang, Zev A Ripstein, John L
> Rubinstein, and Lewis E.Kay 2020”  but I got this error:
> Traceback (most recent call last):
> File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in
> cryosparc2_compute.run.main
> File “cryosparc2_worker/cryosparc2_compute/jobs/var3D/run.py”, line 533,
> in cryosparc2_compute.jobs.var3D.run.run
> File “cryosparc2_worker/cryosparc2_compute/jobs/var3D/run.py”, line 445,
> in cryosparc2_compute.jobs.var3D.run.run.M_step
> File
> “/home/sepideh/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/linalg/linalg.py”,
> line 903, in eigvals
> _assertFinite(a)
> File
> “/home/sepideh/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/linalg/linalg.py”,
> line 217, in _assertFinite
> raise LinAlgError(“Array must not contain infs or NaNs”)
> LinAlgError: Array must not contain infs or NaNs
>  I checked the version of the cryoSPARC they used and I am using the same
> version. According to the paper, I made volume out of the PDB files, and
> then using a simulated data job I got the particle images and did the
> refinement. First I tried the 3D variability using the particles and mask
> from refinement and it seems fine but when I put a mask on N domain as it
> is described in the paper  I got the error.
> I posted the error in cryoSPARC forum but I didn't receive any answer.
> Could you please help me to solve the problem?
>
> Thank you in advance for your help,
> Sepideh
>
> --
>
> *Sepideh Valimehr*
>
> *Graduate Researcher *I* Rouiller Lab*
>
> Department of Biochemistry and Molecular Biology
>
> Bio21 Molecular Science & Biotechnology Institute
>
> The University of Melbourne
>
> *T:* +61 3 83440285 | *E:* sepideh.valimehr at student.unimelb.edu.au
> <ashish.sethi at unimelb.edu.au>
> *I acknowledge the Traditional Owners of the land on which I work, and pay
> my respects to the Elders, past and present.*
>


-- 

*Sepideh Valimehr*

*Graduate Researcher *I* Rouiller Lab*

Department of Biochemistry and Molecular Biology

Bio21 Molecular Science & Biotechnology Institute

The University of Melbourne

*T:* +61 3 83440285 | *E:* sepideh.valimehr at student.unimelb.edu.au
<ashish.sethi at unimelb.edu.au>
*I acknowledge the Traditional Owners of the land on which I work, and pay
my respects to the Elders, past and present.*
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