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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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

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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

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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

Hamidreza Rahmani, Alister Burt3

10/6/25

Removing bad tilts

Thank you for the quick response Alister. I wanted to make sure I am not missing anything here, the

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Removing bad tilts

Thank you for the quick response Alister. I wanted to make sure I am not missing anything here, the

10/6/25

Matt Martinez

10/6/25

Matching Warp/Relion particles with the original Dynamo tags

Hi everyone, I'm trying to match the particles from Warp and Relion 5 refinements back to the

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Matching Warp/Relion particles with the original Dynamo tags

Hi everyone, I'm trying to match the particles from Warp and Relion 5 refinements back to the

10/6/25

Grigory Tagiltsev, Alister Burt2

9/30/25

step back in M

Hi Grigory, You will find a number of files in “versions” folders, at a minimum you should place

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step back in M

Hi Grigory, You will find a number of files in “versions” folders, at a minimum you should place

9/30/25

Niharika Shukla, … Alister Burt8

9/30/25

Defect map does not match image dimensions

Hey Niharika, Really glad you were able to use our packages to solve your issue - thanks also for

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Defect map does not match image dimensions

Hey Niharika, Really glad you were able to use our packages to solve your issue - thanks also for

9/30/25

Peng Liu, Alister Burt5

9/29/25

Issues with particle extraction in Warp

Hi Alister, Thank you for pointing out the concern regarding the signal. We will carefully reassess

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Issues with particle extraction in Warp

Hi Alister, Thank you for pointing out the concern regarding the signal. We will carefully reassess

9/29/25