Re: [COOT] Coot versions
Victor Alves schrieb: Hello Since Ubuntu 9.04 now comes with Python 2.6, is there among the various Coot versions available in Nightly builds, one that comes with GTK2 but not with Python? I hope this is not a very dumb question, but in my ignorance I have these all kind of mixed up, namely which of the various Coot versions available come with GTK1, GTK2, Guile, Python. Any other variations? there is a very simple solution: stop adding things to your $PATH. Instead, use a wrapper script that sets the PATH and other req'd environment variables for the program you want to run. E.g. have the following /usr/local/bin/coot : #!/bin/csh -f setenv PATH /where/ever/coot/was/installed/bin:$PATH setenv COOT_BACKUP_DIR /tmp exec coot $* or some such (I am typing from memory) - you get the idea (you don't have to use csh). In this way you may install as many python versions as your disk can accommodate. One other question. In this link, http://www.ysbl.york.ac.uk/~emsley/coot/build-info Should I not use any builds which are red? What about the size of the green bar? from quick inspection I would guess that green bars mean built less than 24 hours ago and red bar more than 1 day old. Thanks in advance Victor Alves smime.p7s Description: S/MIME Cryptographic Signature
Re: [COOT] 'Isolate' Coot's Python2.6 from Ubuntu system
Victor Alves wrote: Dear all I installed Coot with Python and GTK2 in Ubuntu Intrepid 8.10. Ubuntu 8.10 has Python 2.5. Since 'ccp4-others.setup' file points to Coot's directory when I check 'which python' I get version 2.6 (the one Coot provides). Is there a way to isolate Coot's python from Ubuntu system but still maintaining the ability to call Coot from the terminal? So that Ubuntu's Python version would be the active one for all the system (except for Coot)? Dear Victor, Thank you for reporting this problem. It is not unreasonable for ccp4's setup to add the coot binary directory to the path. However, (as you have noted) Coot adds its built-in python to this directory - and we do that deliberately (but I don't see why, currently). You could try to remove python, python-2.6, python-config and python-2.6-config from that directory and coot should still work fine. Please try this out and let us know if there are problems, I will remove their addition to the binaries if there are not. (Of course, Kay's solution also works - and I do something like that myself, which is why I have not seen this problem). Regards, Paul.
Re: [COOT] Coot versions
Hi Victor, typing from memory is always problematic (in my case at least). My little C wrapper would not work because exec coot $* relies on the $PATH setting, and if that has /usr/local/bin it would call itself recursively. For the record, this is the (actual) /usr/local/bin/coot that we use: #!/bin/csh -f setenv LANG C exec /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot $* BTW the LANG setting solves a problem with the comma (,) versus point (.) interpretation of PDB files (a FAQ). Another BTW: the wrapper technique works nicely for phenix, cns, arpWarp, ... too, and would enable you to use different CCP4 versions in parallel, and so on - you get the idea. HTH, Kay Kay Diederichs schrieb: Victor Alves schrieb: Hello Since Ubuntu 9.04 now comes with Python 2.6, is there among the various Coot versions available in Nightly builds, one that comes with GTK2 but not with Python? I hope this is not a very dumb question, but in my ignorance I have these all kind of mixed up, namely which of the various Coot versions available come with GTK1, GTK2, Guile, Python. Any other variations? there is a very simple solution: stop adding things to your $PATH. Instead, use a wrapper script that sets the PATH and other req'd environment variables for the program you want to run. E.g. have the following /usr/local/bin/coot : #!/bin/csh -f setenv PATH /where/ever/coot/was/installed/bin:$PATH setenv COOT_BACKUP_DIR /tmp exec coot $* or some such (I am typing from memory) - you get the idea (you don't have to use csh). In this way you may install as many python versions as your disk can accommodate. One other question. In this link, http://www.ysbl.york.ac.uk/~emsley/coot/build-info Should I not use any builds which are red? What about the size of the green bar? from quick inspection I would guess that green bars mean built less than 24 hours ago and red bar more than 1 day old. Thanks in advance Victor Alves smime.p7s Description: S/MIME Cryptographic Signature
Re: [COOT] Coot versions
Kay Diederichs wrote: Victor Alves schrieb: One other question. In this link, http://www.ysbl.york.ac.uk/~emsley/coot/build-info Should I not use any builds which are red? What about the size of the green bar? from quick inspection I would guess that green bars mean built less than 24 hours ago and red bar more than 1 day old. That's right. Because the builds happen every night [1] the colours are a hint to us that something may have gone wrong in the daily/nightly builds. I have been thinking about reworking this page, because now that it is used by users (not just developers) it is problematic that a big red bar sometimes represents a quite recent build (as the comment from Victor suggests). Paul. [1] actually, there are exceptions, which make things non-straightforward.
[COOT] monomer DB
Hi all, what is the difference between the monomers db which is provided by coot and the one which is provided by refmac/ccp4? Can one interchange them? thanks justin -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP digital signature
