Search found 240 matches

by jlspzw
Thu Mar 02, 2023 1:11 am
Forum: Main Forum
Topic: TM-align rotation matrix
Replies: 5
Views: 8476

Re: TM-align rotation matrix

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...
by jlspzw
Wed Mar 01, 2023 2:32 pm
Forum: Main Forum
Topic: How can I input multi-chain sequence as fasta?
Replies: 5
Views: 7433

Re: How can I input multi-chain sequence as fasta?

This server will be available after the paper is published.
If you have targets (should not be too much), you can paste them here, and we can manually do them for you.
by jlspzw
Sat Feb 25, 2023 2:07 am
Forum: Main Forum
Topic: 3DRobot Decoys
Replies: 3
Views: 6187

Re: 3DRobot Decoys

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...
by jlspzw
Sat Feb 25, 2023 1:59 am
Forum: Main Forum
Topic: TM-align rotation matrix
Replies: 5
Views: 8476

Re: TM-align rotation matrix

Dear user,

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

Best
IT Team
by jlspzw
Tue Feb 21, 2023 8:52 pm
Forum: Main Forum
Topic: 3DRobot Decoys
Replies: 3
Views: 6187

Re: 3DRobot Decoys

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
by jlspzw
Sun Feb 12, 2023 8:42 pm
Forum: Main Forum
Topic: I-TASSER Illegal division by zero during MUSTER
Replies: 8
Views: 10947

Re: I-TASSER Illegal division by zero during MUSTER

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...
by jlspzw
Mon Feb 06, 2023 3:51 pm
Forum: Main Forum
Topic: I-TASSER Illegal division by zero during MUSTER
Replies: 8
Views: 10947

Re: I-TASSER Illegal division by zero during MUSTER

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
by jlspzw
Sat Feb 04, 2023 10:27 pm
Forum: Main Forum
Topic: I-TASSER Illegal division by zero during MUSTER
Replies: 8
Views: 10947

Re: I-TASSER Illegal division by zero during MUSTER

Dear user, Please download the attached zip file for MUSTER and MUSTER-related programs. 1. unzip the zip files. you will get zal1 zal2 zal3 zal33, add permission by "chmod a+x zal1 zal2 zal3 zal33" 2. go to your I-TASSER/D-I-TASSER programs path, cd bin/MUSTER/bin, backup zal33 by "m...
by jlspzw
Fri Feb 03, 2023 5:30 pm
Forum: Main Forum
Topic: crash on biolip web site and a site at position 0
Replies: 2
Views: 9269

Re: crash on biolip web site and a site at position 0

Dear user,

Which link on the download page did you open?

I check the readme link at https://zhanggroup.org/BioLiP/download.html

It seems I didn't get any problem. The link is https://zhanggroup.org/BioLiP/download/readme.txt

Let me know if you find any issues.

Thank you.

Best
IT Team
by jlspzw
Mon Jan 30, 2023 8:28 pm
Forum: Main Forum
Topic: I-TASSER Internal server error
Replies: 3
Views: 6597

Re: I-TASSER Internal server error

Dear user,

The issue has been solved.

Best
IT Team