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cryoFIT / cryo_fit2

cryo_fit2 source codes, test files, live at .../phenix-xxxx/modules
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can't get cryofit2 to run #13

Open irintom opened 1 year ago

irintom commented 1 year ago

I tried command line installation for Phenix first so that I can choose a destination directory of my preference. Unfortunately my OS (Ventura 13) causes so many security issues and I get so many library load disallowed by system policy issues, and every single time I have to manually enable more than 10 programmes just to run Phenix, yet in the end Phenix wont run complaining it has dependency on something which cannot be opened (because its from an unidentified developer. In the system settings, it wont show 'allow anyway' option even). So I reinstalled my Phenix with point and click installer. This time my installer did not allow me to choose the destination. So it got installed under /Applications with root as owner. However, I was able to get cryo_fit2 into the modules directory of Phenix. Yet when I run libtbx.configure cryo_fit2, the following is the error message I am getting

File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/libtbx/env_config.py", line 3212, in warm_start(sys.argv) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/libtbx/env_config.py", line 3117, in warm_start _warm_start(env, args) File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/libtbx/env_config.py", line 3087, in _warm_start env.refresh() File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/libtbx/env_config.py", line 2213, in refresh completed_file_name.remove() File "/Applications/phenix-1.20.1-4487/modules/cctbx_project/libtbx/path.py", line 275, in remove if self.exists(): os.remove(abs(self)) OSError: [Errno 13] Permission denied: '/Applications/phenix-1.20.1-4487/build/libtbx_refresh_is_completed'

j-prajapati commented 1 year ago

We do not have Ventura yet, so it is hard to reproduce your issues. Moreover, I think you should report the issues with phenix installation to phenix support website, they can help you better in case they have tested with Ventura. Also Cryo_fit2 is not being look after at the moment, because we are busy with adding new features for Cryo_fit1. I suggest to try Cryo_fit1. It is very stable and does the same job. We have been using it for few projects in our group as well. Let me know if there are issues with using Cryo_fit1.