Zhanglab forum

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...

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 ...

9 is the highest

you can check the model*.pdb files, those are the final pdb files of I-TASSER

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.

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...

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

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...

Hi Puja, The P.1 and B.1.351 classification are based on https://cov-lineages.org/, and the representative sequence you can find from our website https://zhanglab.ccmb.med.umich.edu/COVID-19/, see the sequence link. https://zhanglab.ccmb.med.umich.edu/COVID-19/spike/B.1.351/seq.fasta https://zhangla...