Search found 245 matches

by jlspzw
Fri Apr 12, 2024 3:57 pm
Forum: Main Forum
Topic: DeepMSA2 and DMFold questions about DeepMSA2_noIMG.py
Replies: 1
Views: 10

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: 1
Views: 18007

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: 17767

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...
by jlspzw
Sat Mar 30, 2024 2:07 pm
Forum: Main Forum
Topic: Concerns Regarding Delays with DMFold Protein-Protein Interaction Prediction Server
Replies: 4
Views: 16114

Re: Concerns Regarding Delays with DMFold Protein-Protein Interaction Prediction Server

Dear user, We are currently suffering a large number of jobs submitted from the user community, which makes our server job delayed than expected. Please let us know your job ID or email used for submission. We are trying to process the server jobs and make them faster; it may take a couple of days. ...
by jlspzw
Wed Mar 27, 2024 8:27 am
Forum: Main Forum
Topic: dont get results from DeepMSA2
Replies: 1
Views: 9550

Re: dont get results from DeepMSA2

Dear user,

We have recently received a large number of jobs submitted to our server, so your job may take longer than expected. Your job is running now; we hope it can be completed in the next three days.

Best Regards
Wei Zheng
by jlspzw
Wed Mar 27, 2024 8:11 am
Forum: Main Forum
Topic: runtime error in DeepMSA 2.1
Replies: 1
Views: 9672

Re: runtime error in DeepMSA 2.1

Dear yang,

Please check if the memory you requested is enough or not.

Best Regards
Wei Zheng
by jlspzw
Sun Mar 24, 2024 3:30 am
Forum: Main Forum
Topic: what do output colors indicate
Replies: 3
Views: 10599

Re: what do output colors indicate

Dear Maria,

In this case, Jsmol colors the structure from N (blue) to C (red) terminus with a rainbow scale.

Best Regards
Wei Zheng
by jlspzw
Fri Mar 22, 2024 4:48 pm
Forum: Main Forum
Topic: There may be a code error in DMFold's MSA_combination.py
Replies: 1
Views: 9538

Re: There may be a code error in DMFold's MSA_combination.py

Dear Gary,

Thank you for the bug reporting. Yes, it is a typo bug in the code. We have fixed this issue and released new version of DMFold and DeepMSA2 packages.

https://zhanggroup.org/DMFold/download/
https://zhanggroup.org/DeepMSA2/download/

Best Regards
Wei Zheng
by jlspzw
Fri Mar 22, 2024 4:21 pm
Forum: Main Forum
Topic: what do output colors indicate
Replies: 3
Views: 10599

Re: what do output colors indicate

Hi Maria,

What server did you use?

Best Regards
Wei Zheng