Search found 251 matches

by jlspzw
Tue May 07, 2024 10:12 am
Forum: Main Forum
Topic: DMFold
Replies: 2
Views: 985

Re: DMFold

Dear user, The server usually sends the results back to the user in around one week. However, we recently received around 1200 submissions, so the server is overloaded. We are trying to move the jobs to a larger supercomputer cluster, we are expect the current submitted jobs will completed one by on...
by jlspzw
Fri May 03, 2024 8:29 pm
Forum: Main Forum
Topic: Need help for running complex
Replies: 3
Views: 5365

Re: Need help for running complex

Dear user,

We also have a single sequence size limitation, which was 1200 before; I just slightly increased it, so you can submit it now.

Sheng Regards
Wei Zheng
by jlspzw
Tue Apr 30, 2024 6:03 am
Forum: Main Forum
Topic: DMFold
Replies: 1
Views: 1183

Re: DMFold

Dear user, We recently got>1000 submissions from the user community, which is overloading our server. So, the job response time is much longer than usual. We are trying to seek new resources to solve the problem. However, we still need time to set up everything. I have cancel your old job, now you c...
by jlspzw
Tue Apr 30, 2024 5:59 am
Forum: Main Forum
Topic: Need help for running complex
Replies: 3
Views: 5365

Re: Need help for running complex

Dear user,

Please put the sequence here; I will help you check the case.

Best Regards
Wei Zheng
by jlspzw
Wed Apr 17, 2024 4:26 pm
Forum: Main Forum
Topic: Homologous dimer modeling
Replies: 2
Views: 5168

Re: Homologous dimer modeling

Dear user,

You can try https://zhanggroup.org/DMFold/, put two copies of your monomer sequences, and then it is dimmer.

Best Regards
Wei Zheng
by jlspzw
Mon Apr 15, 2024 1:12 pm
Forum: Main Forum
Topic: DMFold Run_DeepMSA2.py error
Replies: 3
Views: 89060

Re: DMFold Run_DeepMSA2.py error

Dear user,

Your change is correct. Please let us know if you have any questions.

Best
Wei
by jlspzw
Fri Apr 12, 2024 3:57 pm
Forum: Main Forum
Topic: DeepMSA2 and DMFold questions about DeepMSA2_noIMG.py
Replies: 1
Views: 45617

Re: DeepMSA2 and DMFold questions about DeepMSA2_noIMG.py

Dear user, DeepMSA2 doesn't contains aMSA, the readme file has some typo, we will delete it from readme. DeepMSA_IMG.py does not require aMSA. qMSA and dMSA is enough for next step. if you only have qMSA.hhb* dMSA.hhb* and do not have d/qMSA.jac* and others, DeepMSA_IMG.py will tell you no need to d...
by jlspzw
Sat Apr 06, 2024 1:09 pm
Forum: Main Forum
Topic: DMFold Run_DeepMSA2.py error
Replies: 3
Views: 89060

Re: DMFold Run_DeepMSA2.py error

Dear user,

You can check the config.py, see the dMSA_cpu setting, etc.

Please try to reduce the CPU number to see if memory can be reduced.

BTW how large is your memory on your Desktop, and how large are your sequences?

Best Regards
Wei Zheng
by jlspzw
Wed Apr 03, 2024 12:41 pm
Forum: Main Forum
Topic: i-TASSER Ab initio FM
Replies: 1
Views: 65479

Re: i-TASSER Ab initio FM

Dear user, You are encouraged to use https://zhanggroup.org/DMFold/ or https://zhanggroup.org/D-I-TASSER/ servers. When using D-I-TASSER, please try to select those three options. Using large IMG/JGI metagenomic database to build MSA (additional one or two days maybe applied). Using AlphaFold2 dista...