Just as an update, I downgraded to Rosetta 3.3 and the same inputs have been working well. It seems like something got broken in this particular application in the upgrade
Hello.
I can’t comment on 3.5, but dr. Chris King had sent me this patch for pepspec for 3.4 earlier, and it had fixed an issue similar to what you’re describing, so maybe try compiling with it? Do backup stuff, though.
If you’re trying it, rename the file in the attachment to pepspec.cc and replace the original pepspec.cc file, then re-compile Rosetta.
Chris King has informed me that the issue should be fixed, and from what I can tell the fix should be included in the 3.5 release.
If you’re still having problem with pepspec with Rosetta 3.5, please provide further details, as it’s likely a different issue from the one encountered by rrphenix in Rosetta 3.4.