Re: [COOT] call for beta testers [was Re: buggy coot 0.6-pre-1 r2264 on OS X 10.4.11]
Dear Paul and Bill, rev 2310 from fink works properly now on mac (intel) os 10.5.8 Thank you a lot for solving this problem so quickly (and heroically)! Some issues, then. When launching coot I get this error: INFO:: loading preferences file /Users/mol/.coot-preferences/ coot_toolbuttons.py Running python script /Users/mol/.coot-preferences/coot_toolbuttons.py Traceback (most recent call last): File string, line 1, in module File /Users/mol/.coot-preferences/coot_toolbuttons.py, line 1, in module coot_toolbar_button(Side-by-side/Mono, side_by_side_stereo_mono_toggle(), stereo-view.svg) NameError: name 'coot_toolbar_button' is not defined and yes, my side-by-side/Mono button is gone (and today I'm unable to find the way to add it back there or to add just any other user- defined button as a matter of fact, but this is most probably because I have less than half neuron awake) Then, a debug warning, I put it here in case it may ring a bell somewhere: load extensions.scm DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c INFO:: loading preferences file /Users/mol/.coot-preferences/coot- preferences.scm Other issues: * Residue Info window is not updated when ab alt-conformation is added * If an alt-conf is added and then an auto-fit-rotamer, the occupancies get mangled (for a two-conf case, one goes to 0.0 occupancy and the other to 1.0) * The labels 'Maximum' and 'minimum distance to protein atoms' in the 'Find waters' dialog are swapped. Or, at least, Minimum is set to 3.40 and maximum to 2.20, which makes no sense to me (but see the neuronal awakeness alert above) And a good thing found in this version: bond parameters preferences (width) is now taken into account!!! Thanks again! Miguel Le 15 sept. 09 à 00:23, Paul Emsley a écrit : On Sep 11, 2009, at 7:36 AM, Benda, Christian wrote: Dear Bill, Thanks for your quick reply! I installed the new revision but it doesn't seem to make a difference (to my problems). I guess you're right and it's because I am still running 10.4 - think it's time to upgrade to 10.6, finally! Again, many thanks and best regards, William G. Scott wrote: Paul just pulled off a heroic fix (rev 2310). Please try that. So the last couple of days have been a bit frustrating for me, but a good deal of credit goes to Bill of course. Anyway... the time is approaching for a new point release. While there are still a couple of issues on the list to be addressed, feedback on the current pre-release would be appreciated. Mac users will need Bill's latest and greatest, others can use the binaries on the pre- release page: http://www.biop.ox.ac.uk/coot/devel/build-info.html If possible, please restrict your comments to issues in 0.6, not missing features or features for 0.7 - there will be time for that after 0.6 is out and working. Thanks, Paul. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I II Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [COOT] call for beta testers [was Re: buggy coot 0.6-pre-1 r2264 on OS X 10.4.11]
Miguel Ortiz Lombardia wrote: Dear Paul and Bill, rev 2310 from fink works properly now on mac (intel) os 10.5.8 Thank you a lot for solving this problem so quickly (and heroically)! Some issues, then. When launching coot I get this error: INFO:: loading preferences file /Users/mol/.coot-preferences/coot_toolbuttons.py Running python script /Users/mol/.coot-preferences/coot_toolbuttons.py Traceback (most recent call last): File string, line 1, in module File /Users/mol/.coot-preferences/coot_toolbuttons.py, line 1, in module coot_toolbar_button(Side-by-side/Mono, side_by_side_stereo_mono_toggle(), stereo-view.svg) NameError: name 'coot_toolbar_button' is not defined Oh dear.. and yes, my side-by-side/Mono button is gone Due to above I guess. Then, a debug warning, I put it here in case it may ring a bell somewhere: load extensions.scm DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c DEBUG:: in safe_python_command_with_return() pValue is 0x162f52c INFO:: loading preferences file /Users/mol/.coot-preferences/coot-preferences.scm Agreed, debug be gone. Other issues: * Residue Info window is not updated when ab alt-conformation is added Fair enough. For 0.6.1 * If an alt-conf is added and then an auto-fit-rotamer, the occupancies get mangled (for a two-conf case, one goes to 0.0 occupancy and the other to 1.0) Confirmed. That's a baddie! - Thanks. * The labels 'Maximum' and 'minimum distance to protein atoms' in the 'Find waters' dialog are swapped. Or, at least, Minimum is set to 3.40 and maximum to 2.20, which makes no sense to me (but see the neuronal awakeness alert above) Shock again! Yes, confirmed. I've had a setting in my .coot file for years, so I've not noticed this. And a good thing found in this version: bond parameters preferences (width) is now taken into account!!! OK. good. Thanks for the feedback.
Re: [COOT] call for beta testers
On Sep 14, 2009, at 3:23 PM, Paul Emsley wrote: So the last couple of days have been a bit frustrating for me, but a good deal of credit goes to Bill of course. This can be read in at least two ways. As anyone who knows me could tell you, the only thing I really can take credit for is constant, relentless complaining.
[COOT] fink remove old packages
Hey all (especially Bill, I guess), I was bushwhacking through the fink jungle on my MacBook Pro (10.5.8) today and realized just how vast it it. There are 18GB in /sw. As examples (and to make this email uncannily on-topic), there are 18 coot_0.6-pre-1-revision--?_darwin-i386.deb packages and 14 coot_0.5-pre-1-*_darwin-i386.deb packages in /sw/fink/10.4/unstable/main/binary-darwin-i386/sci. Is this necessary? How do I clean fink up? I should say that I compile everything from source. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [COOT] ccp4mg
Paul, Thank you for the mail. It is indeed a problem in the PDB format, generated at the Yale server. The segID was wrong and the atom type was missing. After the correction, however, I am still struggling with the animation functions in ccp4mg Zhongren -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:c...@jiscmail.ac.uk] On Behalf Of Paul Emsley Sent: Monday, September 07, 2009 5:04 AM To: COOT@JISCMAIL.AC.UK Subject: Re: ccp4mg Wu, Zhongren wrote: I am using ccp4mg to get nice graphics for presentations. I have no problems to get movie.gif files for structure rotations. However, when use animation, I ran into a lot problems. I followed the instructions closely and get morph files (pdb format) from the yale.edu server. But ccp4mg refuses to take them, complaining the wrong format. I hope somebody can help me out. Hello Zhongren Wu, If ccp4mg complains about the format of the PDB file(s) it is probably right. The devil is in the detail - what does it say? If I had to guess, I'd say that the files from they yale.edu are not sanctioned PDB format. Paul. p.s. slightly ironic that you should ask about ccp4mg here. There is a mailing list for ccp4mg questions: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=CCP4MG
