Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1
Hi, it's me again. With the latest version (1848), I haven't been able to use rotate/translate or rigid body functions (they were fine in 1847, I think). No matter what I set it to, the whole chain gets moved by these functions (even when I set with scripting do_rot_trans_setup to 0, it gets overwritten). I am working on a Mac OS 10.5.6. Does anyone else have a similar experience? Unless you have updated with fink in the last hour, you probably don't have 1848. (Or maybe I should just go to sleep and stop working late hours from home) Thanks everybody, again. Engin William G. Scott wrote: On Feb 5, 2009, at 8:42 PM, Engin Ozkan wrote: P.S. I am starting to like zsh more and more. Me too. zsh is the most fun I have ever had with my clothes on, except possibly when riding the new mountain bike. zsh is to unix shells what OS X is to operating systems. Programmable completions, including remote filename completion with scp alone make it worthwhile. I started a zsh on OS X project, if anyone is interested: http://code.google.com/p/zsh-templates-osx/
Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1
On Feb 5, 2009, at 8:42 PM, Engin Ozkan wrote: P.S. I am starting to like zsh more and more. Me too. zsh is the most fun I have ever had with my clothes on, except possibly when riding the new mountain bike. zsh is to unix shells what OS X is to operating systems. Programmable completions, including remote filename completion with scp alone make it worthwhile. I started a zsh on OS X project, if anyone is interested: http://code.google.com/p/zsh-templates-osx/
Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1
Yep, that fixed it (not that you needed confirming). Thanks a lot. Engin P.S. I am starting to like zsh more and more. William G. Scott wrote: I just discovered that too: tcsh-% coot DISPLAY has been set to /tmp/launch-Oj1wSR/:0 PYTHONPATH: Undefined variable. tcsh-% The problem is really in /sw/bin/coot Edit that file (it is now a wrapper script) and get rid of the spurious \ in the first line. This is the real cause of the problem. zsh and bash apparently cope with it because they are sh-type shells. Sorry, and thanks for finding that problem. Bill On Feb 5, 2009, at 8:30 PM, Engin Ozkan wrote: I am sorry, I forgot to mention, I was actually using tcsh, not bash. And I do have /sw/bin/init.csh source'd (Fink-related everything else seems to work fine anyway). Thanks for looking into it (and maintaining the fink packages). Engin William G. Scott wrote: Hi Engin: Well, I have to confess I only tested it with zsh and tcsh, assuming bash would work the same way. zsh is vastly better than bash, but you are right, it should work equally well on whichever shell the user chooses. So I initiated a bash session, no $PYTHONPATH defined, then source /sw/bin/init.sh and then issued coot and it works. If you don't source /sw/bin/init.sh, it won't work, and many other things in fink will be broken. That is the only thing I can think of. Sorry if that isn't relevant. Are you on 10.4? I don't have access to 10.4 at the moment to test it... Bill On Feb 5, 2009, at 7:50 PM, Engin Ozkan wrote: Hi everyone, I still seem to have issues with fink'ed coot (revision-1847-1). It does not start and it gives an error PYTHONPATH: Undefined variable. I guess I could just define the PYTHONPATH, but I do not have a reason to. More interestingly, if I switch to zsh shell, I don't get the error and coot starts, even though I still don't have the variable defined. Am I missing something here? Thanks, Engin William Scott wrote: Howdie Fulica aficionados: coot-0.6-pre-1-revision-1847-1, available via fink (and my servers as binaries for 10.5), should be working properly now with python2.5. It should also inherit $PYTHONPATH from your environment if you have set that (there is generally no need to, but you may have a reason). HTH, Bill
Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1
I just discovered that too: tcsh-% coot DISPLAY has been set to /tmp/launch-Oj1wSR/:0 PYTHONPATH: Undefined variable. tcsh-% The problem is really in /sw/bin/coot Edit that file (it is now a wrapper script) and get rid of the spurious \ in the first line. This is the real cause of the problem. zsh and bash apparently cope with it because they are sh-type shells. Sorry, and thanks for finding that problem. Bill On Feb 5, 2009, at 8:30 PM, Engin Ozkan wrote: I am sorry, I forgot to mention, I was actually using tcsh, not bash. And I do have /sw/bin/init.csh source'd (Fink-related everything else seems to work fine anyway). Thanks for looking into it (and maintaining the fink packages). Engin William G. Scott wrote: Hi Engin: Well, I have to confess I only tested it with zsh and tcsh, assuming bash would work the same way. zsh is vastly better than bash, but you are right, it should work equally well on whichever shell the user chooses. So I initiated a bash session, no $PYTHONPATH defined, then source /sw/bin/init.sh and then issued coot and it works. If you don't source /sw/bin/init.sh, it won't work, and many other things in fink will be broken. That is the only thing I can think of. Sorry if that isn't relevant. Are you on 10.4? I don't have access to 10.4 at the moment to test it... Bill On Feb 5, 2009, at 7:50 PM, Engin Ozkan wrote: Hi everyone, I still seem to have issues with fink'ed coot (revision-1847-1). It does not start and it gives an error PYTHONPATH: Undefined variable. I guess I could just define the PYTHONPATH, but I do not have a reason to. More interestingly, if I switch to zsh shell, I don't get the error and coot starts, even though I still don't have the variable defined. Am I missing something here? Thanks, Engin William Scott wrote: Howdie Fulica aficionados: coot-0.6-pre-1-revision-1847-1, available via fink (and my servers as binaries for 10.5), should be working properly now with python2.5. It should also inherit $PYTHONPATH from your environment if you have set that (there is generally no need to, but you may have a reason). HTH, Bill
Re: [COOT] Coot GUI [was Re: [ccp4bb] Replacement for arp_waters?]
On 10:04 Fri 30 Jan , Paul Emsley wrote: > There is (of course) only a limited amount of time that we > (collectively) have to work on the code. There are choices to be > made. Do we add a variety of new features [4] or should we add GUI > access to hundreds of esoteric settings and parameters for people who > don't want to read the manual? Yes, there is merit in providing a GUI > for features to functions and parameters previously only available via > scripting [5,6] but it is often not the most valuable thing we can be > doing "right now". Each setting/parameter we have to decide: is this > useful for a typical user or is this just clutter/esoteric/expert-use-only? > > Having said that, the feature mentioned was added in the early days of > Coot - and if it was done today those extra parameters could well be > brought to the GUI surface. Thanks for your response, Paul! I understand what you're saying, and I agree that the focus should be on getting "typical" features into the GUI. The difficulty comes with where to draw the line. It may be that each 10% of users has a different set of typical features, so you can never get things perfect without customizing. > [6] we are also aware that there is also the danger of swamping the > GUI with too many dialogs and boxes - making the important things you > need to find quickly more obscure and hidden. I agree that useless choices should not be choices at all. -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com pgplCQqGRPGBJ.pgp Description: PGP signature
Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1
I am sorry, I forgot to mention, I was actually using tcsh, not bash. And I do have /sw/bin/init.csh source'd (Fink-related everything else seems to work fine anyway). Thanks for looking into it (and maintaining the fink packages). Engin William G. Scott wrote: Hi Engin: Well, I have to confess I only tested it with zsh and tcsh, assuming bash would work the same way. zsh is vastly better than bash, but you are right, it should work equally well on whichever shell the user chooses. So I initiated a bash session, no $PYTHONPATH defined, then source /sw/bin/init.sh and then issued coot and it works. If you don't source /sw/bin/init.sh, it won't work, and many other things in fink will be broken. That is the only thing I can think of. Sorry if that isn't relevant. Are you on 10.4? I don't have access to 10.4 at the moment to test it... Bill On Feb 5, 2009, at 7:50 PM, Engin Ozkan wrote: Hi everyone, I still seem to have issues with fink'ed coot (revision-1847-1). It does not start and it gives an error PYTHONPATH: Undefined variable. I guess I could just define the PYTHONPATH, but I do not have a reason to. More interestingly, if I switch to zsh shell, I don't get the error and coot starts, even though I still don't have the variable defined. Am I missing something here? Thanks, Engin William Scott wrote: Howdie Fulica aficionados: coot-0.6-pre-1-revision-1847-1, available via fink (and my servers as binaries for 10.5), should be working properly now with python2.5. It should also inherit $PYTHONPATH from your environment if you have set that (there is generally no need to, but you may have a reason). HTH, Bill
Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1
Hi Engin: Well, I have to confess I only tested it with zsh and tcsh, assuming bash would work the same way. zsh is vastly better than bash, but you are right, it should work equally well on whichever shell the user chooses. So I initiated a bash session, no $PYTHONPATH defined, then source /sw/bin/init.sh and then issued coot and it works. If you don't source /sw/bin/init.sh, it won't work, and many other things in fink will be broken. That is the only thing I can think of. Sorry if that isn't relevant. Are you on 10.4? I don't have access to 10.4 at the moment to test it... Bill On Feb 5, 2009, at 7:50 PM, Engin Ozkan wrote: Hi everyone, I still seem to have issues with fink'ed coot (revision-1847-1). It does not start and it gives an error PYTHONPATH: Undefined variable. I guess I could just define the PYTHONPATH, but I do not have a reason to. More interestingly, if I switch to zsh shell, I don't get the error and coot starts, even though I still don't have the variable defined. Am I missing something here? Thanks, Engin William Scott wrote: Howdie Fulica aficionados: coot-0.6-pre-1-revision-1847-1, available via fink (and my servers as binaries for 10.5), should be working properly now with python2.5. It should also inherit $PYTHONPATH from your environment if you have set that (there is generally no need to, but you may have a reason). HTH, Bill
Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1
Hi everyone, I still seem to have issues with fink'ed coot (revision-1847-1). It does not start and it gives an error PYTHONPATH: Undefined variable. I guess I could just define the PYTHONPATH, but I do not have a reason to. More interestingly, if I switch to zsh shell, I don't get the error and coot starts, even though I still don't have the variable defined. Am I missing something here? Thanks, Engin William Scott wrote: Howdie Fulica aficionados: coot-0.6-pre-1-revision-1847-1, available via fink (and my servers as binaries for 10.5), should be working properly now with python2.5. It should also inherit $PYTHONPATH from your environment if you have set that (there is generally no need to, but you may have a reason). HTH, Bill
Re: [COOT] Enhancement Request: Ability to add residues into an empty slot in a chain
Schubert, Carsten [PRDUS] wrote: > Would it be possible to enhance the "Change Chain ID.." function to > allow for insertion of residues into an existing chain if the given > resid range is not occupied? if you use the "Use Residue Range" option you can do this. > Could the function be modified in such a way that it checks if the > to be renamed sequence actually fits into its designated slot and > allows the operation and bails if not? The current exclusion scheme is > a bit to broad IMHO. Yes, that would be better than the current situation. However, as there is an alternative path (although not the most obvious, I admit) it is not of the highest priority. Regards, Paul.
[COOT] OS X: coot-0.6-pre-1-revision-1847-1
Howdie Fulica aficionados: coot-0.6-pre-1-revision-1847-1, available via fink (and my servers as binaries for 10.5), should be working properly now with python2.5. It should also inherit $PYTHONPATH from your environment if you have set that (there is generally no need to, but you may have a reason). HTH, Bill
Re: [COOT] Coot crash (0.6-pre-1-revision-1834-10)
I'm in the process of fixing it, but if you want, just edit the file /sw/fink/dists/unstable/main/finkinfo/gnome/pygtk2-gtk-py.info and change the line Type: python (2.5) to Type: python (2.5 2.6) or sit tight for about an hour and I'll have a newer update that works around this problem. You just need it for the python scripting gui window as far as I am aware. I just hate paying so much for this software and having something that isn't absolutely perfect. On Feb 5, 2009, at 3:14 PM, Jonathan Winger wrote: Hi Bill, Forgive my ignorance, but how exactly can I get pygtk2-gtk-py26? I fink-installed python26 and another python package. Incidentally, coot seems to work without the pygtk2-gtk-py26 bit, but I didn't try anything other than launching coot. Thanks, Jon On Feb 5, 2009, at 1:58 PM, William Scott wrote: Sorry. Basically, coot built with python2.6 instead of python2.5. I'll try to fix it the right way, but this one will work if you install fink's python26 and python packages , and then pygtk2-gtk-py26 The catch is there is no pygtk2-gtk-py26 in fink yet (they claim it doesn't work, but it seems fine for coot). So you either have to install my pre-compiled one (the usual way) or hack the info file. On Feb 5, 2009, at 1:53 PM, Jonathan Winger wrote: I get the same message after my fink update to that version of coot. I'm also using OSX10.5.6 on a MacIntel. Anyone find a fix yet? Jon On Feb 5, 2009, at 12:11 PM, S. Shanmuga Sundara Raj wrote: Hi, I updated the Coot pre-release 0.6-pre-1-revision-1834-10 using fink. When I try to run Coot, I am getting the following error. I am using OSX 10.5.6 sssraj% coot dyld: Library not loaded: /sw/lib/python2.6/config/ libpython2.6.dylib Referenced from: /sw/bin//coot Reason: image not found Trace/BPT trap Any suggestions? Thanks Raj
Re: [COOT] Coot crash (0.6-pre-1-revision-1834-10)
Thank you Bill. Updating python to 2.6 solves the problem. Raj --- On Thu, 2/5/09, William Scott wrote: From: William Scott Subject: Re: [COOT] Coot crash (0.6-pre-1-revision-1834-10) To: COOT@JISCMAIL.AC.UK Date: Thursday, February 5, 2009, 4:58 PM Sorry. Basically, coot built with python2.6 instead of python2.5. I'll try to fix it the right way, but this one will work if you install fink's python26 and python packages , and then pygtk2-gtk-py26 The catch is there is no pygtk2-gtk-py26 in fink yet (they claim it doesn't work, but it seems fine for coot). So you either have to install my pre-compiled one (the usual way) or hack the info file. On Feb 5, 2009, at 1:53 PM, Jonathan Winger wrote: I get the same message after my fink update to that version of coot. I'm also using OSX10.5.6 on a MacIntel. Anyone find a fix yet?Jon On Feb 5, 2009, at 12:11 PM, S. Shanmuga Sundara Raj wrote: Hi, I updated the Coot pre-release 0.6-pre-1-revision-1834-10 using fink. When I try to run Coot, I am getting the following error. I am using OSX 10.5.6 sssraj% coot dyld: Library not loaded: /sw/lib/python2.6/config/libpython2.6.dylib Referenced from: /sw/bin//coot Reason: image not found Trace/BPT trap Any suggestions? Thanks Raj
Re: [COOT] Coot crash (0.6-pre-1-revision-1834-10)
Sorry. Basically, coot built with python2.6 instead of python2.5. I'll try to fix it the right way, but this one will work if you install fink's python26 and python packages , and then pygtk2-gtk-py26 The catch is there is no pygtk2-gtk-py26 in fink yet (they claim it doesn't work, but it seems fine for coot). So you either have to install my pre-compiled one (the usual way) or hack the info file. On Feb 5, 2009, at 1:53 PM, Jonathan Winger wrote: I get the same message after my fink update to that version of coot. I'm also using OSX10.5.6 on a MacIntel. Anyone find a fix yet? Jon On Feb 5, 2009, at 12:11 PM, S. Shanmuga Sundara Raj wrote: Hi, I updated the Coot pre-release 0.6-pre-1-revision-1834-10 using fink. When I try to run Coot, I am getting the following error. I am using OSX 10.5.6 sssraj% coot dyld: Library not loaded: /sw/lib/python2.6/config/libpython2.6.dylib Referenced from: /sw/bin//coot Reason: image not found Trace/BPT trap Any suggestions? Thanks Raj
Re: [COOT] Coot crash (0.6-pre-1-revision-1834-10)
I get the same message after my fink update to that version of coot. I'm also using OSX10.5.6 on a MacIntel. Anyone find a fix yet? Jon On Feb 5, 2009, at 12:11 PM, S. Shanmuga Sundara Raj wrote: Hi, I updated the Coot pre-release 0.6-pre-1-revision-1834-10 using fink. When I try to run Coot, I am getting the following error. I am using OSX 10.5.6 sssraj% coot dyld: Library not loaded: /sw/lib/python2.6/config/libpython2.6.dylib Referenced from: /sw/bin//coot Reason: image not found Trace/BPT trap Any suggestions? Thanks Raj
[COOT] Coot crash (0.6-pre-1-revision-1834-10)
Hi, I updated the Coot pre-release 0.6-pre-1-revision-1834-10 using fink. When I try to run Coot, I am getting the following error. I am using OSX 10.5.6 sssraj% coot dyld: Library not loaded: /sw/lib/python2.6/config/libpython2.6.dylib Referenced from: /sw/bin//coot Reason: image not found Trace/BPT trap Any suggestions? Thanks Raj
