[3dem] CryoFIT installation

Kim, Doo Nam doonam at lanl.gov
Wed Feb 14 13:03:48 PST 2018

Hello everyone,

1) Please clone with "git clone git at github.com:cryofit/cryofit.git" at <your phenix>/modules.

For some reason, the clone address was an old one, please use "git clone git at github.com:cryofit/cryofit.git" instead (I already updated in dropbox).

2-1) Please use gromacs-4.5.5_cryoFIT.zip which is a light version.

For those of you who already used 'gromacs-4.5.5_cryo_fit_added', it is fine, just I assumed that it may had taken longer to download.

2-2) gromacs-4.5.5_cryoFIT.zip can be anywhere. It doesn't have to be in ~/src. Living in ~/src wouldn't hurt, just it doesn't have to be.

3) Overall installation process is

- Install phenix

- Link cryoFIT to Phenix (once cryoFIT is released as a public version, this won't be needed, but for now, it is needed)

- Install cryoFIT (which is the modified version of gromacs)

4) Ignore install_openmpi.py

install_openmpi.py lives in 0_install_cryoFIT/obsolete_but_keep_for_furture_use. Literally, it is obsolete to use now. Of course, depending on each system/version, openmpi may be needed. Please email me if you need a troubleshooting.

I appreciate all of your interest/emails so far.

Among those emails/users that I've met, ~10 of them is using cryoFIT well, 2~3 of them is still having trouble with the installation or I lost contact (?).

If you have any comment, suggestions, inquiries, please let us know.

I can't push to phenix developer repository, so there's some inconsistency/lagging between working version and currently pushed version. Once I have an authority to push to phenix developer repository by myself, I expect that I can synchronize everything (at least to the developer version).

Thank you,


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