Antibody homology modeling fails after blastp

This topic has 21 replies, 2 voices, and was last updated 7 years, 7 months ago by Anonymous.

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- February 18, 2017 at 7:25 pm #2586
  Anonymous
  I was following the antibody modeling tutorial on Nature Protocols paper and I wasn’t successful. I followed the tutorial in the Supplementary Material, and got the following error right after performing blastp query. Blast+ was performed well and produced output alright.
  
  libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string
  
  [1] 37692 abort $ROSETTA_BIN/antibody.macosclangrelease -fasta antibody.fasta 95 90
  
  Mac OS version: 10.12.3
  
  Rosetta Version: 3.7 (2016.34)
  
  Blast+ version: 2.6.0
  
  LLVM version: 8.0.0 (clang-800.0.42.1)
  
  And, here’s the files that I used including log files:
  
  https://dl.dropboxusercontent.com/u/163146/tutorial.tar.gz
- February 20, 2017 at 3:39 pm #12148
  Anonymous
  The Antibody team says:
  
  “[You] need the latest weekly [release], as blast changed their output header format”
- February 20, 2017 at 3:39 pm #12669
  Anonymous
  The Antibody team says:
  
  “[You] need the latest weekly [release], as blast changed their output header format”
- February 20, 2017 at 3:39 pm #13190
  Anonymous
  The Antibody team says:
  
  “[You] need the latest weekly [release], as blast changed their output header format”
- February 20, 2017 at 8:49 pm #12150
  Anonymous
  Thanks, I updated Rosetta to 2016.46 and still have the same error message. Or is there a newer build that I’m supposed to use? I’m a commercial user and 2016.46 is the newest build that I’m seeing.
- February 20, 2017 at 8:49 pm #12671
  Anonymous
  Thanks, I updated Rosetta to 2016.46 and still have the same error message. Or is there a newer build that I’m supposed to use? I’m a commercial user and 2016.46 is the newest build that I’m seeing.
- February 20, 2017 at 8:49 pm #13192
  Anonymous
  Thanks, I updated Rosetta to 2016.46 and still have the same error message. Or is there a newer build that I’m supposed to use? I’m a commercial user and 2016.46 is the newest build that I’m seeing.
- February 21, 2017 at 10:33 pm #12153
  Anonymous
  hmm, that does look like the latest release. We had a hiccup in the release system but it must not have restarted smoothly. 3.8 is in the works and will be out before too long. I’ll ping the sysadmin.
- February 21, 2017 at 10:33 pm #12674
  Anonymous
  hmm, that does look like the latest release. We had a hiccup in the release system but it must not have restarted smoothly. 3.8 is in the works and will be out before too long. I’ll ping the sysadmin.
- February 21, 2017 at 10:33 pm #13195
  Anonymous
  hmm, that does look like the latest release. We had a hiccup in the release system but it must not have restarted smoothly. 3.8 is in the works and will be out before too long. I’ll ping the sysadmin.
- February 23, 2017 at 6:09 pm #12155
  Anonymous
  Can you let me know what is the latest Rosetta version available?
  
  Are you one of the author of the manuscript (http://www.nature.com/nprot/journal/v12/n2/abs/nprot.2016.180.html)? I’d like to know what version of Rosetta and blastp was used, but unable to find such information in the manuscript.
- February 23, 2017 at 6:09 pm #12676
  Anonymous
  Can you let me know what is the latest Rosetta version available?
  
  Are you one of the author of the manuscript (http://www.nature.com/nprot/journal/v12/n2/abs/nprot.2016.180.html)? I’d like to know what version of Rosetta and blastp was used, but unable to find such information in the manuscript.
- February 23, 2017 at 6:09 pm #13197
  Anonymous
  Can you let me know what is the latest Rosetta version available?
  
  Are you one of the author of the manuscript (http://www.nature.com/nprot/journal/v12/n2/abs/nprot.2016.180.html)? I’d like to know what version of Rosetta and blastp was used, but unable to find such information in the manuscript.
- February 23, 2017 at 6:54 pm #12156
  Anonymous
  The problem that’s been holding up releases has been resolved. It’s looking likely we will process one this Friday. (Well, we’ll definitely process one, it has a good chance of passing the automated tests).
- February 23, 2017 at 6:54 pm #12677
  Anonymous
  The problem that’s been holding up releases has been resolved. It’s looking likely we will process one this Friday. (Well, we’ll definitely process one, it has a good chance of passing the automated tests).
- February 23, 2017 at 6:54 pm #13198
  Anonymous
  The problem that’s been holding up releases has been resolved. It’s looking likely we will process one this Friday. (Well, we’ll definitely process one, it has a good chance of passing the automated tests).
- February 26, 2017 at 5:27 pm #12159
  Anonymous
  A new weekly is up, give it a try.
- February 26, 2017 at 5:27 pm #12680
  Anonymous
  A new weekly is up, give it a try.
- February 26, 2017 at 5:27 pm #13201
  Anonymous
  A new weekly is up, give it a try.
- February 27, 2017 at 7:02 pm #12161
  Anonymous
  Thanks, I updated to vesion 2017.8 and the protocol started working.
  
  Best,
  
  Sunhwan
- February 27, 2017 at 7:02 pm #12682
  Anonymous
  Thanks, I updated to vesion 2017.8 and the protocol started working.
  
  Best,
  
  Sunhwan
- February 27, 2017 at 7:02 pm #13203
  Anonymous
  Thanks, I updated to vesion 2017.8 and the protocol started working.
  
  Best,
  
  Sunhwan
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