Search found 157 matches
- Tue Sep 05, 2023 5:43 am
- Forum: Main Forum
- Topic: problem in running demo
- Replies: 25
- Views: 532725
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?
- Sun Sep 03, 2023 6:26 am
- Forum: Main Forum
- Topic: problem in running demo
- Replies: 25
- Views: 532725
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
/media/ravis/data/DEMO/DEMO-2.0/run_DEMO2.py 1dquA /media/ravis/data/DEMO/1dquA /media/ravis/data/DEMO/1dquA/1dquA/seq.fasta
- Fri Sep 01, 2023 3:56 am
- Forum: Main Forum
- Topic: problem in running demo
- Replies: 25
- Views: 532725
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...
- Thu Aug 31, 2023 10:52 am
- Forum: Main Forum
- Topic: problem in running demo
- Replies: 25
- Views: 532725
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...
- Thu Aug 31, 2023 2:11 am
- Forum: Main Forum
- Topic: problem in running demo
- Replies: 25
- Views: 532725
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...
- Sun Aug 27, 2023 1:46 am
- Forum: Main Forum
- Topic: probelm in demo2
- Replies: 1
- Views: 21588
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, ....
2. You can ignore them.
Please remember the domain files should be named as dom1.pdb, dom2.pdb, ....
- Sun Aug 27, 2023 1:45 am
- Forum: Main Forum
- Topic: problem in running demo
- Replies: 1
- Views: 12559
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.
2. You can ignore them.
- Thu Aug 24, 2023 7:57 am
- Forum: Main Forum
- Topic: problem in running demo
- Replies: 1
- Views: 6557
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 ...
- Tue Jun 14, 2022 1:50 am
- Forum: Main Forum
- Topic: Predicted model using ITASSER software
- Replies: 1
- Views: 4106
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...
- Tue Jun 14, 2022 1:45 am
- Forum: Main Forum
- Topic: Final model predicted by the software
- Replies: 1
- Views: 3845
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...