Zhanglab forum

Dear user,

Our staff finds you posted this question by email, so he will answer your question by email. Thank you.

Best
IT Team

Dear user, your question has been addressed by email.

Dear user,

FASPR can only add a side-chain to the protein target.

Best
IT Team

Dear user, If so, you may use the -o option of TM-align/TM-score, then you can get the superposed structures (structure1 aligned to structure2), for example -o sup Then you will have sup sup_atm etc. files, load the sup_atm (maybe need to re-name it as sup_atm.pdb) by PyMOL, and then you will get th...

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If you have targets (should not be too much), you can paste them here, and we can manually do them for you.

Dear user, I got your points, since you only get 443 decoys while you want to 1000, so I guess your program may not be correctly completed, could you check if the default hour 48 is enough for your case? you can set -hour 240 hours to see if things changed. you can see 8A is 2/5 range of 20A, 443 is...

Dear user,

You can use -m matrix.txt to output the matrix.

Best
IT Team

Dear user,

I am slightly confused. If you want 1000 decoys with RMSD<8A, then why not set the threshold as 8A?

Best
IT Team

Dear Jim, We seem to find the issue of your case. Please find the attached updated main D-I-TASSER program. You can unzip the file and put the binary file dcasdpo4v2.1 to $pkgdir/I-TASSERmod/ (replace the old one), then re-run the main I-TASSER program, If you want to try to debug testing with the f...

Hi Jim,

Could you send me the input and output files you get for this case. I will check what's the issue.

You can either attach to this forum or send it to me by email (zhengwei@umich.edu)

BTW, for the DEP issue, please check if re-downloading the ITlib helps.

Best
IT Team