error downloading trained cath model and sw model

[nicoleamorveli]

--2024-05-15 09:29:56-- https://users.flatironinstitute.org/~thamamsy/tm_vec_swiss_model.ckpt Reusing existing connection to users.flatironinstitute.org:443. HTTP request sent, awaiting response... 403 Forbidden 2024-05-15 09:29:56 ERROR 403: Forbidden.

--2024-05-15 09:29:56-- https://users.flatironinstitute.org/thamamsy/public_www/tm_vec_swiss_model_params.json Resolving users.flatironinstitute.org (users.flatironinstitute.org)... 144.121.86.48 Connecting to users.flatironinstitute.org (users.flatironinstitute.org)|144.121.86.48|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: /~thamamsy/tm_vec_swiss_model_params.json [following]

--2024-05-15 09:37:46-- https://users.flatironinstitute.org/thamamsy/public_www/tm_vec_cath_model.ckpt Resolving users.flatironinstitute.org (users.flatironinstitute.org)... 144.121.86.48 Connecting to users.flatironinstitute.org (users.flatironinstitute.org)|144.121.86.48|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: /~thamamsy/tm_vec_cath_model.ckpt [following] --2024-05-15 09:37:47-- https://users.flatironinstitute.org/~thamamsy/tm_vec_cath_model.ckpt Reusing existing connection to users.flatironinstitute.org:443. HTTP request sent, awaiting response... 403 Forbidden 2024-05-15 09:37:47 ERROR 403: Forbidden.

--2024-05-15 09:37:47-- https://users.flatironinstitute.org/thamamsy/public_www/tm_vec_cath_model_params.json Resolving users.flatironinstitute.org (users.flatironinstitute.org)... 144.121.86.48 Connecting to users.flatironinstitute.org (users.flatironinstitute.org)|144.121.86.48|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: /~thamamsy/tm_vec_cath_model_params.json [following] --2024-05-15 09:37:47-- https://users.flatironinstitute.org/~thamamsy/tm_vec_cath_model_params.json Reusing existing connection to users.flatironinstitute.org:443. HTTP request sent, awaiting response... 403 Forbidden 2024-05-15 09:37:47 ERROR 403: Forbidden.

it worked well for deep blast model

[mortonjt]

Hi thanks for raising this issue. We are currently shuffling around datasets. The TMvec models and databases can be found here : https://github.com/flatironinstitute/deepblast/issues/160

[nicoleamorveli]

Thank you very much! I'm just having problems with the link https://zenodo.org/deposit/11199459 for downloading databases

[mortonjt]

Thanks, try https://zenodo.org/records/11199459 instead (it was a typo before)

[GXY0116]

Thanks, try https://zenodo.org/records/11199459 instead (it was a typo before)

Hi thanks for raising this issue. We are currently shuffling around datasets. The TMvec models and databases can be found here : flatironinstitute/deepblast#160

Hi, are there tm-vec swiss model links that we can download, I haven't found any in issues

[mortonjt]

Hi give it a shot now. The swissprot model has been uploaded

On Fri, Jul 5, 2024 at 3:56 AM GXY0116 @.***> wrote:

Thanks, try https://zenodo.org/records/11199459 instead (it was a typo before)

Hi thanks for raising this issue. We are currently shuffling around datasets. The TMvec models and databases can be found here : flatironinstitute/deepblast#160 https://github.com/flatironinstitute/deepblast/issues/160

Hi, are there tm-vec swiss model links that we can download, I haven't find any in issues

— Reply to this email directly, view it on GitHub https://github.com/tymor22/tm-vec/issues/38#issuecomment-2210385829, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXOHCRBJSD2DY22SLH3ZKZGUNAVCNFSM6AAAAABHXZEJKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQGM4DKOBSHE . You are receiving this because you commented.Message ID: @.***>

[GXY0116]

Hi give it a shit now. The swissprot model has been uploaded … On Fri, Jul 5, 2024 at 3:56 AM GXY0116 @.> wrote: Thanks, try https://zenodo.org/records/11199459 instead (it was a typo before) Hi thanks for raising this issue. We are currently shuffling around datasets. The TMvec models and databases can be found here : flatironinstitute/deepblast#160 <flatironinstitute/deepblast#160> Hi, are there tm-vec swiss model links that we can download, I haven't find any in issues — Reply to this email directly, view it on GitHub <#38 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXOHCRBJSD2DY22SLH3ZKZGUNAVCNFSM6AAAAABHXZEJKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJQGM4DKOBSHE . You are receiving this because you commented.Message ID: @.>

Thanks, but I only find cath tmvec models here(https://figshare.com/articles/dataset/TMvec_DeepBLAST_models/25810099), totally 3 files.

[mortonjt]

Looks like I forgot to click "publish", there should be 5 files now

[GXY0116]

Looks like I forgot to click "publish", there should be 5 files now

Thanks, now it works

[yfyi-hub]

tm_vec_swiss_model_large.ckpt tm_vec_swiss_model_large_params.json tm_vec_cath_model_large.ckpt tm_vec_cath_model_large_params.json This 4 files still can't be downloaded

[mortonjt]

Can you provide a more detailed error message? I haven't heard of folks have issues with the figshare download up until now

[yfyi-hub]

Figshare is OK.But the model weights/config of the large TM-vec model trained on SwissModel pairs and the model weights/config of the large TM-vec model trained on CATH pairs can't be found in figshare.

https://users.flatironinstitute.org/~thamamsy/tm_vec_swiss_model_large.ckpt Reusing existing connection to users.flatironinstitute.org:443. HTTP request sent, awaiting response... 403 Forbidden 2024-08-28 11:15:28 ERROR 403: Forbidden.

[mortonjt]

Hi, I'm not sure where you are getting those URLs from. Those have been broken for a while and won't be fixed.

The swiss-prot model should be on figshare.

[yfyi-hub]

In both your article and GitHub's README.md document, you have a total of four models, but I was only able to download two of them on your figshare. You wrote in your article that The TM-Vec models trained on CATHS40 and SWISS-MODEL chains up to 300 residues long both had 17.3 million trainable parameters and were 199MB in size. These models contained two transformer encoder layers. The TM-Vec models trained on CATHS100 domains (ProtTucker training domains) and SWISS-MODEL chains (up to 1,000 residues long) both had 34.1 million trainable parameters and were 391 MB in size.

[mortonjt]

Hi thanks for following up @yfyi-hub all 4 TMvec models are now available on the figshare link. Feel free to give it a shot

[mortonjt]

I'm closing this issue since it should have been resolved. There is a new figshare link : https://figshare.com/s/e414d6a52fd471d86d69