Zhanglab forum

Dear Sheila, Our server recently had a large amount of submissions so the pending time of the job is longer than usual, also the time shown on the output page is an estimated running time. Based on our checking, your job is just starting to run, please give the server more time to complete the job. ...

Dear user,

Sorry for the lateness, our server recently has had many submissions, so the job pending is longer than usual, based on my checking, your job is running, and it may take another 2-3 days to complete. Thank you.

Best Regards
IT Team

Hi Shijie, Thank you for the suggestion. First, we want to clarify, that although pTMscore is overall trustable, it still has some problems, especially when compared to different version AF2 models. For example, version 2.1 pTMscore is higher than version 2.2 in most cases, but the real performance ...

Hi Xin-Dong, Please see the structure comparison results of your local model (yellow+green) and server model (purple) First, based on my checking, the pLDDT score of those two models is around 0.75, which is >0.7 indicating they are correct backbone folds but may not be perfect as pLDDT ranges from ...

Dear user,

Thank you for your sequence, we will test the case and let you know the answer soon.

Best Regards
Wei Zheng

Hi Shijie, Based on my knowledge, it should be still the Jax problem with RTX4090 card, since we do not have that card we never tried if AF2 could run with RTX4090. now I think we need some time to see if Deepmind has any solution https://github.com/google-deepmind/alphafold/issues?q=is%3Aissue+is%3...

Hi Xin-Dong, Could you also send me your local version model (ideally also including the MSAs), I will see the difference. BTW, from the model, I can see the terminal helix seems without contact with other parts, so it is possible that the orientation between the terminal helix with other parts has ...

Dear user,

This is interesting, could you send me your input sequences, I will test with your case.

Best
Wei

Dear user, Please do the following and I will check if the files are correctly generated. 1. check what files exist in your MSA and JGI folder. 2. check if DeepJGI.aln/a3m q3JGI.aln/a3m q4JGI.aln/a3m exists in the JGI folder? (those files should be the results of this step) 3. when running the progr...

Dear Shijie, Thank you for using our software, we only test the program on A40, V100, and A100 GPU cards, and never tried RTX4090, so I am not sure I can help with this issue. But have you ever tried this ticket https://zhanggroup.org/forum/viewtopic.php?f=3&t=1010&sid=5e1ad01058db09c1807abd...