- phenixbb - phenix-online.org

Re: [phenixbb] PHENIX installation issues
by Ralf W. Grosse-Kunstleve 14 Mar '06

14 Mar '06

> > Another thing is i installed in a user so whenever i do project it > gives permission denied . I suspect you have the following situation: drwx------ 2 rwgk cci 4096 Mar 14 10:47 phenix-1.1a I.e. when you installed phenix the "umask" was set such that "group" and/or "others" don't have read permission. Please verify my suspicion with ls -d $PHENIX If you see the "drwx------" or maybe "drwxr-x---" it is easy to fix. Use the su command to become root, then: find phenix-1.1a -exec chmod go+r {} \; find phenix-1.1a -type d -exec chmod go+x {} \; Cheers, Ralf

1 0

PHENIX installation issues
by Peter Zwart 14 Mar '06

14 Mar '06

I see. Unfortunately, the switching between bash and csh is needed until the next release. I am not quite sure what this > Another thing is i installed in a user so whenever i do project it gives permission denied . error/problem exactly is or how it can be solved, but maybe some of my collegues have an idea. Peter Ethayathulla Abdulsamath wrote: > hi Petrus: > > yes, it got installed I replied in phenixbb. > > But problem is everytime i have to do csh then source phenix_env file. > Then again change back to bash. > > Another thing is i installed in a user so whenever i do project it > gives permission denied . > > Everytime i logged in root then do thinz IS there any sol for it >

1 0

Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Ralf W. Grosse-Kunstleve 13 Mar '06

13 Mar '06

> > how to change bash setup ot csh. > > I guess you can change shell (type csh or so) in a single window for > installing, sourcing Exactly. > and running phenix. Not necessarily. This trick should work: bash prompt $ csh csh prompt % source phenix_env csh prompt % bash bash prompt $ Providing a phenix_env.sh is on our todo list. Cheers, Ralf

1 0

Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Petrus H Zwart 13 Mar '06

13 Mar '06

> how to change bash setup ot csh. I guess you can change shell (type csh or so) in a single window for installing, sourcing and running phenix. > In ccp4 there is a file for everything but how to i do for Phenix ! Yes. It is a bit clumsy, I agree. However note that the release you have is still an alpha release (http://en.wikipedia.org/wiki/Development_stage), indicating that not everything is as much in place as one might like it to be. Let us know if you have any (additional) problems. HTH Peter _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

1 0

Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Ethayathulla A.S 12 Mar '06

12 Mar '06

Dear peter: how to change bash setup ot csh. I understood that the program is written for csh and tcsh how do change to bash format so that it gets installed In ccp4 there is a file for everything but how to i do for Phenix ! Thanking you Ethayathulla

1 0

Re: [phenixbb] Regarding installation
by Petrus H Zwart 10 Mar '06

10 Mar '06

Hai Ethayathulla, Have a look at the following posting: http://www.phenix-online.org/pipermail/phenixbb/2006- February/000004.html i.e., things do not work in bash, but do in csh/tcsh. HTH Peter Hi I tried to install Phenix in RED HAT 9.0 LINUX It got installed succesfully But when tried to source it gives error message bash :/ command not found :/usr/local/phenix1.1a/phenix_env line 38 unexpected end of line plz suggest Thanking you -- A.S.Ethayathulla Department of BIophysics All India Institute of Medical Sciences Ansai Nagar New Delhi-110029 India _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

1 0

Regarding installation
by Ethayathulla A.S 10 Mar '06

10 Mar '06

Hi I tried to install Phenix in RED HAT 9.0 LINUX It got installed succesfully But when tried to source it gives error message bash :/ command not found :/usr/local/phenix1.1a/phenix_env line 38 unexpected end of line plz suggest Thanking you -- A.S.Ethayathulla Department of BIophysics All India Institute of Medical Sciences Ansai Nagar New Delhi-110029 India

1 0

Re: [phenixbb] bug? iotbx.reflection_statistics apparent
by Ralf W. Grosse-Kunstleve 06 Mar '06

06 Mar '06

> I tried supplying the space group in the command line using the > --symmetry I think there is another bug there - the command line > symmetry does not override the (wrong) symmetry that the routine gets > from the .sca file I am afraid you are right again. I forgot to include the plumbing for the --force_symmetry option. Sorry, this is getting ugly. To use your unmerged reflection file, edit this Python script in the iotbx tree: echo `libtbx.show_dist_paths iotbx`/iotbx/scalepack/no_merge_original_index.py Replace all "force_symmetry=False" with "force_symmetry=True", then try again.

1 0

Re: [phenixbb] bug? iotbx.reflection_statistics apparent space group error reading scalepack .sca file
by Ralf W. Grosse-Kunstleve 06 Mar '06

06 Mar '06

> iotbx.reflection_statistics returns space group 195 > for a scalepack 'no merge original index' .sca file for > space group 123 (i.e space group 197) > > the first line of the .sca file is > 12 i23 You are right, this is a bug. Sorry. However, it went unnoticed because we usually supply the correct space group (along with the missing unit cell parameters) via --symmetry=some_other_file You could also use --unit_cell=10,20,30,90,90,90 --space_group=197 Mostly I prefer --symmetry because there is less of a chance to mistype. Also, quite often the space group in a reflection file is not correct anyway (e.g. P222 vs. P212121). > the CCP4 program scala can output a 'no merge original index' format > file, which has all 24 i23 symmetry operators in the header - but > iotbx.reflection_statistics cannot read that either I think you should be able to use the .sca file with the --symmetry or --space_group option. I've never tried to work with scala 'no merge original index' files. If you could send me your files I will look into fixing both problems. Peter Zwart wrote: > Note that iotbx.reflection statistics itself performs a merging step, > which is less sophisticated then those available in SCALA or scalepack. > Therefor, it might be worthwile considering supplying merged data to > iotbx.reflection_statistics. That's right. The simple merging in the cctbx is meant to be a stop-gap measure. It is best to merge externally with a program specifically designed for this purpose. Thanks for reporting the bug! Cheers, Ralf

2 1

bug? iotbx.reflection_statistics apparent space group error reading scalepack .sca file
by Peter Metcalf 06 Mar '06

06 Mar '06

Hi - I hope this is the right place to post this iotbx.reflection_statistics returns space group 195 for a scalepack 'no merge original index' .sca file for space group 123 (i.e space group 197) the first line of the .sca file is 12 i23 the CCP4 program scala can output a 'no merge original index' format file, which has all 24 i23 symmetry operators in the header - but iotbx.reflection_statistics cannot read that either cheers Peter Metcalf

1 0