Dear user,
you can download the C-QUARK package at https://zhanglab.dcmb.med.umich.edu/C-Q ... nload.html
Best
ITteam
Search found 251 matches
- Tue Jul 06, 2021 5:44 pm
- Forum: Main Forum
- Topic: how to download QUARK locally?
- Replies: 4
- Views: 2676
- Mon Jul 05, 2021 2:10 pm
- Forum: Main Forum
- Topic: Problems with C-QUARK standalone
- Replies: 11
- Views: 13567
Re: Problems with C-QUARK standalone
If the python has issue, then you can try /bin/python2 /mnt/disk/C-QUARK-1.0/contact/DeepMSA/scripts/build_MSA.py /mnt/disk/C-QUARK-1.0/example/seq.fasta -hhblitsdb=/mnt/disk/ITLIB/uniclust30/uniclust30_2017_04 -jackhmmerdb=/mnt/disk/ITLIB/uniref90/uniref90.fasta -hmmsearchdb=/mnt/disk/ITLIB/metaclu...
- Mon Jul 05, 2021 2:08 pm
- Forum: Main Forum
- Topic: Problems with C-QUARK standalone
- Replies: 11
- Views: 13567
Re: Problems with C-QUARK standalone
Dear user, During the program running, there are many files created by the program will locate in /tmp/skyto and /tmp/. Do NOT and make sure your system will NOT clean those two folders! It is not difficult to run DeepMSA you can do export HHLIB=/mnt/disk/C-QUARK-1.0/contact/DeepMSA then run /mnt/di...
- Mon Jul 05, 2021 1:53 pm
- Forum: Main Forum
- Topic: Errors in threading programs in standalone C-I-TASSER-1.0
- Replies: 3
- Views: 3904
Re: Errors in threading programs in standalone C-I-TASSER-1.0
Dear user, It may be caused by some uncomplete library file could you do "ls /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/ITLIB2" and "ls /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/ITLIB2/summary" see if ...
- Sun Jul 04, 2021 11:28 pm
- Forum: Main Forum
- Topic: How to specify secondary structure on downloaded I-TASSER?
- Replies: 3
- Views: 4092
Re: How to specify secondary structure on downloaded I-TASSER?
9 is the highest
- Tue Jun 29, 2021 5:23 pm
- Forum: Main Forum
- Topic: How to directly convert I-TASSER output into .pdb files
- Replies: 2
- Views: 3651
Re: How to directly convert I-TASSER output into .pdb files
you can check the model*.pdb files, those are the final pdb files of I-TASSER
- Tue Jun 29, 2021 5:20 pm
- Forum: Main Forum
- Topic: Can FDpred standalone version work with proteins whose length > 1,500 aa?
- Replies: 6
- Views: 6422
Re: Can FDpred standalone version work with proteins whose length > 1,500 aa?
FUpred can handle the protein with large 1,500AA by standalone version, if you do not want to wait, you can try it by your computer.
- Tue Jun 29, 2021 5:17 pm
- Forum: Main Forum
- Topic: How to specify secondary structure on downloaded I-TASSER?
- Replies: 3
- Views: 4092
Re: How to specify secondary structure on downloaded I-TASSER?
Hi DavidB256, Unfortunately, the standalone version I-TASSER do not support self-defined secondary structure by commands. However you can modify by replace the seq.dat file in your data folder before doing I-TASSER simulation. here is one example of seq.dat file 39 GLN 4 3 40 LYS 4 7 41 VAL 4 7 42 V...
- Tue Jun 29, 2021 5:00 pm
- Forum: Main Forum
- Topic: What if I have no academic email accoun?
- Replies: 2
- Views: 2924
Re: What if I have no academic email accoun?
Hi zhangzhou,
If you want to use the structure and function prediction service, you can try https://zhanglab.dcmb.med.umich.edu/C-I-TASSER/ or https://zhanglab.dcmb.med.umich.edu/LOMETS/, which accept non-academic email .
Thank you for using our services.
Best
IT team
If you want to use the structure and function prediction service, you can try https://zhanglab.dcmb.med.umich.edu/C-I-TASSER/ or https://zhanglab.dcmb.med.umich.edu/LOMETS/, which accept non-academic email .
Thank you for using our services.
Best
IT team
- Tue Jun 29, 2021 4:58 pm
- Forum: Main Forum
- Topic: Problems with C-QUARK standalone
- Replies: 11
- Views: 13567
Re: Problems with C-QUARK standalone
Hi skyto, The problem occurs on DeepMSA stage, I guess you may try to clean /tmp/skyto/ during the job running, based on you log file, it seems DeepMSA running correctly, but some output files are lost during the job running. So please clean the example folder (only left the seq.fasta file) and re-r...