Zhanglab forum

Dear Xiaogen
Thanks for your immediate response. I used the example file(1dquA) to run the Demo from the training folder. This folder contains these files: demo1.pdb, demo2.pdb, pdb.pdb and seq.fasta(Figure1). when I opened seq.fasta file, it just contained the whole sequence of pdb.pdb file not each domain separately (dom1 and dom2) (Figure2)
1- How can I make the domain file because it did not exist this file in the 1qquA folder? would you mind sending me the example files for running the Demo?
2-how should I introduce the domain file and seq.fasta file in the demo running command? is the below command according to these files correct?
/media/ravis/data/DEMO/DEMO-2.0/run_DEMO2.py 1dquA seq.fasta -template dom1.pdb dom2.pdb
thanks for helping me
Best regards

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/demo1/1dquA".

Please let me know if you have any questions.

Thanks,
Xiaogen

Dear Xiaogen
thanks for your answer. What should seq.fasta file have? should it contains the sequence file of each domain or whole sequence of target protein?
in addition in your example command in your DEMO package the -template icon has exists. please see the below command:
run_DEMO2.py name input_dir seq.fasta -template /nfs/example/template.pdb
what about .pdb files? how should I introduce them?

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 library.

Thanks.

Dear Xiaogen
So if the seq.fasta file is the whole sequence of target protein how can I should introduce my domain file(dom1 and dom2 sequence file) in the DEMO command as you sent me?
/media/ravis/data/DEMO/DEMO-2.0/run_DEMO2.py 1dquA D:/demo/demo1 D:/demo/demo1/seq.fasta
because with this command line I faced this error:"Use the given template to guide the assembly. there is 0 (<2) domain in /media/ravis/data/DEMO/1dquA/seq.fasta" because the seq.fasta file according to that told me contains the whole sequence of target and in your command no flag was existed for introducing domain file.
also, I have two templates of each domain file in PDB format as dom1.pdb and dom2.pdb. so how could I introduce this two pdb file by flag -template in the command?
best regards

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 this file.

"-template" is used to input the full-chain templates rather than domain templates. If you do not have the domain PDB file but have the templates, you can firstly model the domain structures using I-TASSER by providing your templates, then assemble them using DEMO.

You can also use our I-TASSER-MTD server for automatic multi-domain structure modelling. You just need to input the full-chain sequence to the server. Optionally, you can also input the domain definition you have.

Thanks.

Dear Xiaogen
I ran the Demo-2 package by the below command:(Figure 1)
/media/ravis/data/DEMO/DEMO-2.0/run_DEMO2.py 1dquA /media/ravis/data/DEMO/1dquA/1dquA/seq.fasta
the seq. fasta file that contained the whole sequence of the target protein but the Demo program did not run again. What is the problem
Thanks for helping me
best regards

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

Dear Xiaogen
Thanks for your answer. I ran DEMO by the command that you sent me and I got this error: the library is not complete please check it(Figure1). when I searched in the DEMO package I did not find the library directory except lib and lib64(figure2). so, I put the library files in the local _library directory that I made in the DEMO package(Figure3) and I set the library path in run_DEMO2.py file like this:
NR_DB = "/nfs/amino-library/nr/nr" #NR database
hhblitsdb = "/nfs/amino-home/zhng/local_library/uniclust30_2017_04/uniclust30_2017_04"
jackhmmerdb = "/nfs/amino-home/zhng/local_library/uniref90/uniref90.fasta"
hmmsearchdb = "/nfs/amino-home/zhng/local_library/metaclust/metaclust_2017_05.clean.fasta"
MDlibpath = "/nfs/amino-home/zhanglabs/DEMO/multidomain_protein_CA" #where the multi-domain protein library is
runstyle = "semiparallel" # parallel sbatch all jobs. semiparallel sbatch some jobs.
is this correct or I should put the library files in lib or lib64 directory?
thanks if you help me with this issue
best regards

I think it might be an issue with the hhbilitsdb library. Could you please open the 'uniclust30' folder and show me its contents?