#Alpha zip download for mac code
Lastly, there was some code reorganization that doesn't affect the user, just the maintainability. The appl圜ontactsWithin was also not working properly, and has also been fixed - also this command now appears in the ref guide, whereas before it was effectively secret. The scrubber didn't always behave properly - I fixed this and also removed the setForceAndStericScrubber parameter. Unfortunately MMB no longer guesses missing backbone atom information.Ī couple of bugs which may have affected 2.9.2 users have been fixed. The accuracy and speed issues associated with coordinate matching in earlier releases are now solidly addressed. matchFast now works even with normal-precision, standard PDB files, and is in fact the only matching method permitted. In this release, reading in PDB files and generating internal coordinate models based on them, is MUCH faster. Lastly, we have moved from subversion to git. You can have your input files in there, and also write output persistently. This mounts your current directory in the docker container.
#Alpha zip download for mac install
Install docker ( ) and then issue:ĭocker run -v $(pwd):/work -it samuelflores/mmb-ubuntu:3.0ĭocker run -v $(pwd):/work -it samuelflores/mmb-ubuntu:latest But you might prefer a docker container which runs MMB 3.0 like a dream. Lastly, we slightly updated NtC parameters.īinaries are provided below. In 3.0, we introduced the Planck's-Law noise generator. Version 2.19 has the difference that it reads triclinic density maps. These improve the conformational parameters of consecutive bases, for instance to form double helices. In the 2.18 release, Emanuel Peter, Bohdan Schneider, and Jiri Cerny implemented their Nucleotide Conformers (NtC's). You can have your input files in the image's /work directory, and also write output persistently. Install docker ( ) and then issue: docker run -v $(pwd):/work -it samuelflores/mmb-ubuntu:3.0 Or if you like living on the edge: docker run -v $(pwd):/work -it samuelflores/mmb-ubuntu:latest This mounts your current directory in the docker container. If you are a Linux or Mac user, we remind you that Docker images are available for trunk and several named releases on dockerhub: samuelflores/mmb-ubuntu. There are some undocumented features to help fit DNA in icosohedral viruses, contact us if you work on that.įor simple nucleic acid folding problems, you should try our easy to use server at. It can also read and write mmCIF structure files (not just PDB). Thanks to Michal Tykac, MMB can now read MRC density maps. Since version 2.19 MMB reads triclinic density maps. This builds on the earlier release in which Emanuel Peter and Jiri Cerny implemented their Nucleotide Conformers (NtC's) and includes updated parameters.