Warp

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Install Warp on Linux: conda create -n warp warp -c warpem -c nvidia/label/cuda-11.8.0 -c pytorch -c conda-forge

GitHub

Documentation

To report bugs, please use GitHub Issues

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Mingyu Jung, Ricardo Righetto3

8:47 AM

Tomogram deconvolution in Warp

Dear Ricardo Thank you for your help. It really helps. Best, Mingyu 2026년 1월 27일 화요일 AM 12시 50분 46초

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Tomogram deconvolution in Warp

Dear Ricardo Thank you for your help. It really helps. Best, Mingyu 2026년 1월 27일 화요일 AM 12시 50분 46초

8:47 AM

Alister Burt, … joe dobbs5

3:44 AM

taking a break

Hi Alister, Your help has been crucial for a really large number of people, and I echo the others in

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taking a break

Hi Alister, Your help has been crucial for a really large number of people, and I echo the others in

3:44 AM

Kyle Messina, … Matt Martinez10

Jan 26

Error Trying to Perform FS Motion and CTF Correction

Hi Marten, Forgot to get back about this. I definitely am not familiar with all the complexities, but

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Error Trying to Perform FS Motion and CTF Correction

Hi Marten, Forgot to get back about this. I definitely am not familiar with all the complexities, but

Jan 26

Hamidreza Rahmani, Reika Watanabe2

Jan 23

Qestion on MCore models

Hello! My questions might be somewhat related to Hamid's question. I have several independent

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Qestion on MCore models

Hello! My questions might be somewhat related to Hamid's question. I have several independent

Jan 23

Maurice Frijns, Marten Chaillet4

Jan 19

Difference in alignment quality between StandAlone Aretomo3 and the Aretomo3 wrapper inside WarpTools

Hi Maurice, I think you're right that it's not updated. I ran the AreTomo3 wrapper this

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Difference in alignment quality between StandAlone Aretomo3 and the Aretomo3 wrapper inside WarpTools

Hi Maurice, I think you're right that it's not updated. I ran the AreTomo3 wrapper this

Jan 19

P C

12/31/25

Noise2Map options for final map denoising

Happy New Year! What options are used in M to produce denoised maps? I am trying to apply Noise2Map

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Noise2Map options for final map denoising

Happy New Year! What options are used in M to produce denoised maps? I am trying to apply Noise2Map

12/31/25

Dylan Noone, Sylvain Trepout6

12/20/25

Worker process did not connect within the allotted time.

Hi Dylan, Great that you found a solution. In my case, there was an error on the cluster filesystem

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Worker process did not connect within the allotted time.

Hi Dylan, Great that you found a solution. In my case, there was an error on the cluster filesystem

12/20/25

Mart Last, … Alister Burt6

12/15/25

ts_export_particles without raw data

Thank you for reporting back Mart, this is ugly and I'm sorry it's necessary but glad you

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ts_export_particles without raw data

Thank you for reporting back Mart, this is ugly and I'm sorry it's necessary but glad you

12/15/25

B Wimmer, … Jeff Songrong Qu9

12/5/25

Subtomogram Reconstruction - Striping Artifact

Dear all, Thanks again for the input! We have also been trying to use relion5/4 for the same particle

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Subtomogram Reconstruction - Striping Artifact

Dear all, Thanks again for the input! We have also been trying to use relion5/4 for the same particle

12/5/25

Zhu Qiao, … Marten Chaillet7

12/4/25

Warptools reconstruction and denoise

Hi Paris, Thanks for the reply! What we saw was more akin to the second screenshot of the original

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Warptools reconstruction and denoise

Hi Paris, Thanks for the reply! What we saw was more akin to the second screenshot of the original

12/4/25

Peng Liu, … Alister Burt6

11/17/25

Correcting lamella pre-tilt after autoalign_dynamo alignment

Dear Alister, Thank you very much for your information. It sounds exciting that we have this new

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Correcting lamella pre-tilt after autoalign_dynamo alignment

Dear Alister, Thank you very much for your information. It sounds exciting that we have this new

11/17/25

Charlie, Pranav Shah2

11/14/25

Helical refinement in M

Yes. Recommend reprocessing your subset data (with target assemblies) in warptools Best, Pranav --

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Helical refinement in M

Yes. Recommend reprocessing your subset data (with target assemblies) in warptools Best, Pranav --

11/14/25

Clare Trahan2

11/11/25

Recommendation For My Neighbors !!!

@anyone interested??? On Monday, November 10, 2025 at 6:11:48 AM UTC-8 Clare Trahan wrote: Hey

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Recommendation For My Neighbors !!!

@anyone interested??? On Monday, November 10, 2025 at 6:11:48 AM UTC-8 Clare Trahan wrote: Hey

11/11/25

Chris, Alister Burt2

11/7/25

warp env pulls PyTorch 2.0.1 (cu118) (built against NumPy 1.x); NumPy 2.x (current default on conda-forge)

hey Chris, Thanks for the note, I think we only link against the C++ library behind torch so don'

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warp env pulls PyTorch 2.0.1 (cu118) (built against NumPy 1.x); NumPy 2.x (current default on conda-forge)

hey Chris, Thanks for the note, I think we only link against the C++ library behind torch so don'

11/7/25

Miles Graham, … Alister Burt16

11/5/25

Imod vs warp reconstruction - tilt series alignments import query

Hi, Semantics of what the values mean are completely different in each case - in IMOD they're

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Imod vs warp reconstruction - tilt series alignments import query

Hi, Semantics of what the values mean are completely different in each case - in IMOD they're

11/5/25

Paris Watson, Alister Burt4

10/28/25

Refinement in MCore - Choosing parameters

Congratulations! Great work :-) You can do it but it might be a pain - have to go back and re-export

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Refinement in MCore - Choosing parameters

Congratulations! Great work :-) You can do it but it might be a pain - have to go back and re-export

10/28/25

HUGO MUÑOZ HERNÁNDEZ, … Alister Burt8

10/27/25

MCore failed after a while running

2000 tilt series!!!! Good luck and sorry there isn't an easier method for resuming from crashes -

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MCore failed after a while running

2000 tilt series!!!! Good luck and sorry there isn't an easier method for resuming from crashes -

10/27/25

Dylan Noone, Alister Burt7

10/23/25

Problems with WarpTools ts_aretomo

Works, thanks! On Thursday, 23 October 2025 at 16:57:09 UTC+1 alist...@gmail.com wrote: Sorry,

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Problems with WarpTools ts_aretomo

Works, thanks! On Thursday, 23 October 2025 at 16:57:09 UTC+1 alist...@gmail.com wrote: Sorry,

10/23/25

马卓妍, Alister Burt2

10/23/25

M estimateweights error

Hi Alice, Looks like a bug, sorry about that! We'll fix if we can reproduce locally - you

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M estimateweights error

Hi Alice, Looks like a bug, sorry about that! We'll fix if we can reproduce locally - you

10/23/25

Peng Liu, Alister Burt2

10/21/25

Switching Warp versions and individual image removal

Hi Peng, I recommend reprocessing to avoid potential issues but understand this is a bit of a

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Switching Warp versions and individual image removal

Hi Peng, I recommend reprocessing to avoid potential issues but understand this is a bit of a

10/21/25

Laina Nicole Hall, Alister Burt2

10/20/25

Template matching issue

Hey Laina, Your image hasn't come through so hard to tell what's going on but a few questions

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Template matching issue

Hey Laina, Your image hasn't come through so hard to tell what's going on but a few questions

10/20/25

P C, Wanlong Hu5

10/17/25

peristent error

the new version seems to do much better, with fewer crashes. Thank you. On Tuesday, October 14, 2025

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peristent error

the new version seems to do much better, with fewer crashes. Thank you. On Tuesday, October 14, 2025

10/17/25

Irene Hu, … Alister Burt5

10/17/25

cuFFT error in WarpTools template matching on large tomogram

Hi Alister, Thanks so much for the reply — that makes a lot of sense! I was benchmarking to see

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cuFFT error in WarpTools template matching on large tomogram

Hi Alister, Thanks so much for the reply — that makes a lot of sense! I was benchmarking to see

10/17/25

Juan Carlos De la Concepción, … Kewei Gu20

10/13/25

Particle recentering from Relion to Warp

Thank you so much! On Monday, October 13, 2025 at 9:51:06 PM UTC+8 alist...@gmail.com wrote: Oh and

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Particle recentering from Relion to Warp

Thank you so much! On Monday, October 13, 2025 at 9:51:06 PM UTC+8 alist...@gmail.com wrote: Oh and

10/13/25

Hamidreza Rahmani, teg...@gmail.com6

10/13/25

Padding in MCore refinement

Update on this: my GPU could manage as low as 1.4A. However, I could not perform frame refinement

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Padding in MCore refinement

Update on this: my GPU could manage as low as 1.4A. However, I could not perform frame refinement

10/13/25

Wanlong Hu, Alister Burt13

10/13/25

Help troubleshooting Relion5 Refine3D crash with Warp-processed tomo particles

Hi Wanlong, I'm glad you got sorted, great work and thanks for sharing publicly! Cheers, Alister

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Help troubleshooting Relion5 Refine3D crash with Warp-processed tomo particles

Hi Wanlong, I'm glad you got sorted, great work and thanks for sharing publicly! Cheers, Alister

10/13/25

Maurice Frijns, … teg...@gmail.com7

10/13/25

Is dose weighting performed on tiltseries in WarpTools?

Hi Dimitri and Alister, Thanks for the responses, very insightful! Cheers, Maurice Op ma 13 okt 2025

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Is dose weighting performed on tiltseries in WarpTools?

Hi Dimitri and Alister, Thanks for the responses, very insightful! Cheers, Maurice Op ma 13 okt 2025

10/13/25

P C, Alister Burt4

10/10/25

simple transformation of a star file

Hi Peter, Probably best to just manipulate your input star file before import into M, here is my

unread,

simple transformation of a star file

Hi Peter, Probably best to just manipulate your input star file before import into M, here is my

10/10/25

P C, Alister Burt2

10/7/25

physical overlap of species

Overlapping density is not modelled explicitly and the low resolution information in your data will

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physical overlap of species

Overlapping density is not modelled explicitly and the low resolution information in your data will

10/7/25

P C, Alister Burt3

10/6/25

refine_stageangles

thank you! On Tuesday, October 7, 2025 at 12:41:44 AM UTC+1 alist...@gmail.com wrote: Hi Peter, Your

unread,

refine_stageangles

thank you! On Tuesday, October 7, 2025 at 12:41:44 AM UTC+1 alist...@gmail.com wrote: Hi Peter, Your

10/6/25