Search found 251 matches

by jlspzw
Fri Feb 09, 2024 6:31 pm
Forum: Main Forum
Topic: Run Run_DeepMSA2.py issue
Replies: 9
Views: 14535

Re: Run Run_DeepMSA2.py issue

Dear user, Sorry for the late reply, we have tested your sequences and found the issue. Now new versions of DeepMSA2 (v2.1) and DMFold (v1.1) have been online, we have fixed a couple of issues including the one you find. Thank you. https://zhanggroup.org/DMFold/download https://zhanggroup.org/DeepMS...
by jlspzw
Sat Feb 03, 2024 2:36 pm
Forum: Main Forum
Topic: Query regarding DMfold-Multimer software for predicting protein complex
Replies: 4
Views: 6342

Re: Query regarding DMfold-Multimer software for predicting protein complex

Dear user, It is difficult to say the exact running time because different device running time is different. So I would suggest you test the program on your own cluster. Normally MSA will take less than 1 day if you have enough CPUs and modeling will take less than 1 day (<1000AA) if you have enough...
by jlspzw
Fri Feb 02, 2024 3:11 pm
Forum: Main Forum
Topic: Regarding pLDDT
Replies: 1
Views: 4390

Re: Regarding pLDDT

Dear user,

The residue level pLDDT should be available in the download model file, see the beta factor column in the PDB file.

Best Regards
Wei Zheng
by jlspzw
Fri Feb 02, 2024 3:07 pm
Forum: Main Forum
Topic: Query regarding DMfold-Multimer software for predicting protein complex
Replies: 4
Views: 6342

Re: Query regarding DMfold-Multimer software for predicting protein complex

Dear user, we do not have any statistical data about dimmer, but we have data with protein length with DMFold server https://zhanggroup.org/DMFold/help.html Notice, that is our server running time which should differ from the local version (without pending time), so typically standalone should be mu...
by jlspzw
Mon Jan 29, 2024 12:50 pm
Forum: Main Forum
Topic: How do you Delete/Remove/Cancel Server Jobs?
Replies: 2
Views: 5435

Re: How do you Delete/Remove/Cancel Server Jobs?

Dear user,

C-QUARK jobs have been completed, you can assess them by

https://zhanggroup.org/C-QUARK/output/QB3559/
https://zhanggroup.org/C-QUARK/output/QB3617/

Your FG-MD and EvoDesign jobs have been canceled, now you can submit new jobs.

Best Regards
IT Team
by jlspzw
Wed Jan 24, 2024 11:55 am
Forum: Main Forum
Topic: Results not available from COACH server
Replies: 1
Views: 5746

Re: Results not available from COACH server

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. ...
by jlspzw
Fri Jan 19, 2024 7:36 am
Forum: Main Forum
Topic: Runtime Question
Replies: 1
Views: 6585

Re: Runtime Question

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
by jlspzw
Thu Jan 18, 2024 7:30 am
Forum: Main Forum
Topic: Problem with installing DMFoldv1
Replies: 5
Views: 8451

Re: Problem with installing DMFoldv1

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 ...
by jlspzw
Thu Jan 18, 2024 7:16 am
Forum: Main Forum
Topic: Issue Encountered While Setting Up DMFold
Replies: 13
Views: 15942

Re: Issue Encountered While Setting Up DMFold

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 ...
by jlspzw
Thu Jan 18, 2024 7:00 am
Forum: Main Forum
Topic: Run Run_DeepMSA2.py issue
Replies: 9
Views: 14535

Re: Run Run_DeepMSA2.py issue

Dear user,

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

Best Regards
Wei Zheng