Search found 240 matches

by jlspzw
Wed Jan 17, 2024 3:59 am
Forum: Main Forum
Topic: Issue Encountered While Setting Up DMFold
Replies: 13
Views: 6659

Re: Issue Encountered While Setting Up DMFold

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 ...
by jlspzw
Wed Jan 17, 2024 3:55 am
Forum: Main Forum
Topic: Run Run_DeepMSA2.py issue
Replies: 9
Views: 4314

Re: Run Run_DeepMSA2.py issue

Dear user,

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

Best
Wei
by jlspzw
Wed Jan 17, 2024 1:20 am
Forum: Main Forum
Topic: Run Run_DeepMSA2.py issue
Replies: 9
Views: 4314

Re: Run Run_DeepMSA2.py issue

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...
by jlspzw
Tue Jan 16, 2024 9:59 am
Forum: Main Forum
Topic: Problem with installing DMFoldv1
Replies: 5
Views: 3470

Re: Problem with installing DMFoldv1

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...
by jlspzw
Tue Jan 16, 2024 9:54 am
Forum: Main Forum
Topic: Run Run_DeepMSA2.py issue
Replies: 9
Views: 4314

Re: Run Run_DeepMSA2.py issue

Dear user,

You can ignore this warning, this is may be you run the program two times, and the first time those links are created, the program should run without a problem when you see this message. Let us know if you have any other trouble.

Best Regards
Wei Zheng
by jlspzw
Tue Jan 16, 2024 9:52 am
Forum: Main Forum
Topic: No confirmation or reply mail
Replies: 14
Views: 74791

Re: No confirmation or reply mail

Hi Zijian,

Yes, please change to another email address, some emails seem to have issues with receiving our notification email, we think it is an issue from your email server side, and can not be solved by our side. Thank you.

Best Regards
Wei Zheng
by jlspzw
Sun Jan 14, 2024 8:36 am
Forum: Main Forum
Topic: No confirmation or reply mail
Replies: 14
Views: 74791

Re: No confirmation or reply mail

Dear Zijian,

We have sent the jobs to your email. and maybe next time you should change another email. Thank you.

Best Regards
Wei Zheng
by jlspzw
Sat Jan 13, 2024 4:18 am
Forum: Main Forum
Topic: No confirmation or reply mail
Replies: 14
Views: 74791

Re: No confirmation or reply mail

Dear Zijian,

We didn't find you have jobs running on DMFold, you can test submit your job again.

BTW, try to clean your input sequence, despite we have implemented the non-ascii code dealing function, we suggest only containing the 'English word' in your input information.

Best Regards
Wei Zheng
by jlspzw
Fri Jan 12, 2024 5:27 am
Forum: Main Forum
Topic: Issue Encountered While Setting Up DMFold
Replies: 13
Views: 6659

Re: Issue Encountered While Setting Up DMFold

Hi Xin-Dong,

Yes, sometimes the amber refinement has an issue with GPU, you can either use CPU to do refinement (it still has some change failed) or cancel it and use other tools to remove clash (if exists).

Glad to see you solve the problems.

Best
Wei
by jlspzw
Thu Jan 11, 2024 8:12 am
Forum: Main Forum
Topic: Issue Encountered While Setting Up DMFold
Replies: 13
Views: 6659

Re: Issue Encountered While Setting Up DMFold

Hi Xin-Dong Based on the message I guess it may be the issue from Google Jax, You can try a different version Jax, if you used CUDA11, maybe pip install absl-py==0.13.0 biopython==1.79 chex==0.0.7 dm-haiku==0.0.4 dm-tree==0.1.6 immutabledict==2.0.0 jax==0.2.14 ml-collections==0.1.0 numpy==1.20.1 sci...