Search found 157 matches

by xiaogenz
Tue Sep 05, 2023 5:43 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 487025

Re: problem in running demo

I think it might be an issue with the hhbilitsdb library. Could you please open the 'uniclust30' folder and show me its contents?
by xiaogenz
Sun Sep 03, 2023 6:26 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 487025

Re: problem in running demo

Because you missed one input. Please use the following command for your case:

/media/ravis/data/DEMO/DEMO-2.0/run_DEMO2.py 1dquA /media/ravis/data/DEMO/1dquA /media/ravis/data/DEMO/1dquA/1dquA/seq.fasta
by xiaogenz
Fri Sep 01, 2023 3:56 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 487025

Re: problem in running demo

Hello, DEMO is used when the 3D structure of the domain is known. The domain definition is included in the pdb file of the domain. You should name each domain pdb file as "dom1.pdb, dom2.pdb, ..." and put them in "D:/demo/demo1/1dquA" in your case. The program will find them from...
by xiaogenz
Thu Aug 31, 2023 10:52 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 487025

Re: problem in running demo

Hello, seq.fasta is the whole sequence of target protein. We give the usage of DEMO2 in line 96 of README.TXT rather than line 105. -template is the option when you have a good template. You can ignore it if you have not template, and the algorithm will identify templates from the multi-domain libra...
by xiaogenz
Thu Aug 31, 2023 2:11 am
Forum: Main Forum
Topic: problem in running demo
Replies: 25
Views: 487025

Re: problem in running demo

Hello, You can run it using the following command: /media/ravis/data/DEMO/DEMO-2.0/run_DEMO2.py 1dquA D:/demo/demo1 D:/demo/demo1/seq.fasta Please note that "D:/demo/demo1" is the directory shown in your Figure2. The second input should be "D:/demo/demo1" instead of "D:/demo...
by xiaogenz
Sun Aug 27, 2023 1:46 am
Forum: Main Forum
Topic: probelm in demo2
Replies: 1
Views: 11830

Re: probelm in demo2

1. DEMO-EM is run when you need to use cryo-EM density maps. You can ignore it or change its directory to DEMO-EM2.
2. You can ignore them.

Please remember the domain files should be named as dom1.pdb, dom2.pdb, ....
by xiaogenz
Sun Aug 27, 2023 1:45 am
Forum: Main Forum
Topic: problem in running demo
Replies: 1
Views: 6534

Re: problem in running demo

1. DEMO-EM is run when you need to use cryo-EM density maps. You can ignore it or change its directory to DEMO-EM2.
2. You can ignore them.
by xiaogenz
Thu Aug 24, 2023 7:57 am
Forum: Main Forum
Topic: problem in running demo
Replies: 1
Views: 3185

Re: problem in running demo

Hello Ladan Mafakher, As the "README.txt" file described, you also should download NR database and multi-domain protein structure library from the DEMO download page. It is correct to create a folder to save all the library, but you should change the corresponding variables in lines 55-59 ...
by xiaogenz
Tue Jun 14, 2022 1:50 am
Forum: Main Forum
Topic: Predicted model using ITASSER software
Replies: 1
Views: 3057

Re: Predicted model using ITASSER software

"top 5 final model" shows the final I-TASSER predicted model for your target sequence. " top 10 Identified stuctural analogs in PDB" shows the templates that may have similar structure to your target sequence, which are found in PDB. These templates are used to guide the structur...
by xiaogenz
Tue Jun 14, 2022 1:45 am
Forum: Main Forum
Topic: Final model predicted by the software
Replies: 1
Views: 2846

Re: Final model predicted by the software

Yes. Models shown in the "Final Full-length Models Predicted by I-TASSER-MTD" part is the final and full model predicted by I-TASSER-MTD. "Top 10 Full-length Templates for Domain Assembly" just shows the templates used to guide the domain assembly for the full-length model constr...