Re: [COOT] Coot Book of the Genesis
Bernhard, the CentOS5 binaries used to work well on RHEL6 /CentOS6/ SL6 ; there was a glitch a few weeks ago which was fixed after I reported it ( https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=coot;31d9d7f5.1201 ). I install the latest nightly build every couple of months / weeks, and this works very well. So for those who are not interested in learning to build coot (including me) the binaries are the way to go. If the CentOS5 binary needs libraries on RHEL6 /CentOS6/ SL6 , this can be fixed in the way that applies to all s/w packages: from the error message, find the name of the library; yum install ; repeat until success. Works very well, even with a mix of 32bit and 64bit libraries. good luck, Kay
Re: [COOT] broken icons on Red Hat 5 (but not on Red Hat 6)
Dear Ben and Coot developers, > I have an installation of Coot 0.7-pre-1-r3633 for 64-bit linux installed > on to an NFS share at /programs/x86_64-linux/coot/0.7-pre-1-r3633. This is > the CentOS 5 64-bit build provided by Paul. > > On Red Hat 5, 3 of the icons in the righthand toolbar are missing: > Rotamers, Flip Peptide and Alternate Conformation icons. I encountered the same problem since it remains in rev 3999. After some struggling, I found a way to fix the problem. Replace 16 svg files in share/coot/pixmaps/ with the attached ones. It seems a bug in libsvg, since these problematic files cannot be displayed correctly by ImageMagick command (display) on my RedHat 5 system. In SVG path data, lineto commands can be omitted if they follow a moveto command (*). However, these implicit lineto are ignored, which is the cause. Therefore, I explicitly added lineto commands (L or l) in path data of svg. (*) http://www.w3.org/TR/SVG11/paths.html#PathDataMovetoCommands > If a moveto is followed by multiple pairs of coordinates, > the subsequent pairs are treated as implicit lineto commands. Regards, Takaaki Fukami - Dr. Takaaki Fukami (mailto:fukami...@chugai-pharm.co.jp) Discovery Research Dept. (Biostructure Gr.) Roche Group: Chugai Pharmaceutical Co.,Ltd. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Ben Eisenbraun Sent: Tuesday, October 04, 2011 11:47 PM To: COOT@JISCMAIL.AC.UK Subject: Re: broken icons on Red Hat 5 (but not on Red Hat 6) On Tue, Oct 04, 2011 at 11:03:53AM +0200, Bernhard Lohkamp wrote: > > Are only the icons missing or the button as well? Only the icons. If you mouse-over the spot, it highlights and you get the pop up help and the button works. > Missing icons (only) is a bit more mysterious since the mentioned ones > are not special. I.e. the only ones in another format (svg or png), so > the libraries seem to be in place and functioning for the other icons > (usual suspects: svg-loader, pixbuf-loaders). A bit puzzling. Indeed. I copied undo.svg over rotamers.svg, and that icon will load properly. I can also duplicate this on our 32-bit installation, same Coot version, tested on CentOS 5 and Scientific Linux 6. My user reported the problem doesn't exist in the 0.6.2 release. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | fixed_icons.tgz Description: fixed_icons.tgz
Re: [COOT] clean install on RHEL 6.2
On 09/02/12 07:10, Bernhard Rupp (Hofkristallrat a.D.) wrote: Dear Cootsies, following Paul's advice I started to autobuild coot using http://lmb.bioch.ox.ac.uk/coot/build-install-coot-from-scratch.html It is a little bit like whacking hamsters - it needs swig, which needs pcre... Sorry about this. RHEL 6.x binaries should be available shortly after I get back [1]. I have a such a machine under my desk now. I need to make the release for 0.7, Find a monitor and keyboard and switch for the beastie, Then I can log in, run the script and feel your pain. I would have thought (without checking) that yum would provide a sufficiently recent swig to make coot compile script happy... not so much manual begetting? Paul. [1] from Melbourne.
Re: [COOT] clean install on RHEL 6.2
I found why the RHEL package isn't being built and publicly available - it will take some time to sort out, sorry about that. Regards, Tim On Wed, Feb 8, 2012 at 6:55 PM, Tim Fenn wrote: > coot should be available via yum (albeit 0.6.2) - if there is a > problem with the el package, file a bug report - or feel free to use > the rpm file as an alternative guide to building it: > > http://pkgs.fedoraproject.org/gitweb/?p=coot.git > > HTH, > Tim > > On Wed, Feb 8, 2012 at 12:39 PM, Tim Gruene wrote: >> -BEGIN PGP SIGNED MESSAGE- >> Hash: SHA1 >> >> Install the developer packages of gtk-2.0 and glib-2.0 !?!? >> Sorry for an obvious suggestion but you don't say whether or not you've >> deon that. >> >> Tim >> >> On 02/08/2012 09:10 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: >>> Dear Cootsies, >>> >>> following Paul's advice I started to autobuild coot using >>> http://lmb.bioch.ox.ac.uk/coot/build-install-coot-from-scratch.html >>> >>> It is a little bit like whacking hamsters - it needs swig, which needs >>> pcre... >>> >>> Ok then it gets going, but an error appears >>> >>> 2012-02-08 10:45:46 (67.0 KB/s) - >>> ?/root/coot/autobuild/sources/guile-gtk-2.1.tar.gz? saved [781985/781985] >>> awk: cmd. line:1: fatal: cannot open file >>> `/usr/include/gtk-2.0/gtk/gtkversion.h' for reading (No such file or >>> directory) >>> >>> which seems to be a guile version conflict and >>> rears its ugly head when upon ./config make from the newly created package >>> I get >>> >>> checking for GLIB... configure: error: Package requirements (glib-2.0) were >>> not met: >>> No package 'glib-2.0' found >>> >>> I think these problems are connected and I wonder how they can be fixed? >>> >>> Best regards, BR >>> - >>> Bernhard Rupp >>> 001 (925) 209-7429 >>> +43 (676) 571-0536 >>> b...@ruppweb.org >>> hofkristall...@gmail.com >>> http://www.ruppweb.org/ >>> - >>> No animals were hurt or killed during the >>> production of this email. >>> - >>> >> >> - -- >> Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> -BEGIN PGP SIGNATURE- >> Version: GnuPG v1.4.10 (GNU/Linux) >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >> >> iD8DBQFPMt1xUxlJ7aRr7hoRAuvuAJ96MVx/9Ue2XzyrNOduqijavSdklwCfaein >> d7tEFjbWDByBZrOogaAy8N0= >> =gPNG >> -END PGP SIGNATURE-
Re: [COOT] Coot Book of the Genesis
Hi folks: I think the best long-term solution for this is to get coot and all of its non-standard-linux dependencies into the repositories of the most frequently used linux distribution systems. If this isn't possible, then at least create our own repositories for these packages, so that they are accessible to debian utilities (for Ubuntu Linux, standard Debian Linux, etc), and the other major package management systems. (For OS X, we use the fink-based debian package management system in three ways: 1. In its official capacity, to build coot and all of its dependencies from scratch 2. I host (unofficial) repositories for 10.6 and 10.7, so users can install pre-compiled debian packages 3. I use it to create automatic nightly builds of a "stand-alone" package ). I am pretty sure Donnie Berkholtz did this for gentoo already. I think at the very least we should aim to do this for ubuntu already. Is anyone reading this a maintainer for ubuntu and/or debian? Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax:+1-831-4593139 (fax) On Feb 9, 2012, at 3:49 AM, Bernhard Rupp (Hofkristallrat a.D.) wrote: > ...because the precompiled binary from the Coot site looks for some > libraries it (and I) cannot find (see that January thread 'Help needed...' > on the subject) > and the suggestion there is to 'do it right and build from scratch'. > > But if you have another link to a RHEL binary I am happy to try again... > > Thx, BR > > -Original Message- > From: Frank Thommen [mailto:structures...@embl-heidelberg.de] > Sent: Thursday, February 09, 2012 1:17 AM > To: COOT@JISCMAIL.AC.UK > Cc: b...@hofkristallamt.org > Subject: Re: Coot Book of the Genesis > > ...and why not simply use the binary RHEL 5 version? At least the CentOS 5 > binary distribution works fine on CentOS 6. > > Why making one's life harder than needed? > > Cheers > > frank > > Frank Thommen - Structures IT Management and Support - EMBL Heidelberg > structures...@embl-heidelberg.de - +49 6221 387 8353
Re: [COOT] using custom key bindings in wincoot ( where to put .cootrc or equivalent in coot for windows)
Thanks Bernhard, Sorry for not reading your very clear instructions properly. ..My monitor resolution was set crazy high and I missed the dot before the coot.py Once I renamed my key-bindings to dot-coot-dot-py (.coot.py) and placed them into the C:\Wincoot directory..the key bindings work on startup. Thanks again Hari On Thu, Feb 9, 2012 at 3:50 AM, Bernhard Lohkamp wrote: > > Hi Hari, > > the file (in your $HOME) directory should be called .coot.py > (dot-coot-dot-py). The dot in front is important (*)!!! coot.py is a very > different file which is read in somewhere else. > Alternatively put your coot.py file in the directory > $HOME/.coot-preferences/ (again watch out for the dot!, in case the > directory doesnt already exist). > > B > > (*) On Windows there may be the problem to rename it using the explorer. The > DOS shell should allow you to do so. > > >> Hello Bernhard, >> Thanks for your email . >> >> It turns out that my file was not called coot.py and I also had a few >> "hidden" new-line characters due to a copy paste from your wiki python >> key bindings. >> Once I named the file coot.py and corrected the python syntax..I see >> the following behavior: >> >> At startup I do have windows coot inform me that it read in coot.py. >> However the key bindings do not work and do not show up in the User >> key bindings listing. Also activating a shortcut gives a "Key 119is >> not bound message" >> >> If I now read in the same coot.py using the Menu-Run-Script-select >> coot.py. The key-bindings then get registered and show up in the >> listing and work just great. >> >> >> So there is something..maybe in the order the python files are read in >> ..but having a valid coot.py file didnt add the key bindings at >> startup. >> >> I am wondering how I can avoid reading the key bindings in every time >> manually. >> >> Thanks >> Hari >> >> >> On Wed, Feb 8, 2012 at 2:57 AM, Bernhard Lohkamp >> wrote: >>> >>> >>> Hi Hari, >>> >>> python scripts are read in from the following locations (*)(x): >>> >>> - $HOME/.coot.py (equivalent to .coot) >>> - $HOME/.coot-preferences (a directory, all script file from here are >>> read) >>> - $COOT_PYTHON_EXTRAS_DIR (a directory which you can specify yourself) >>> >>> Calculate->Run script should always work. If it doesnt there may be >>> something wrong with the script. What does the DOS console tell you. >>> >>> Hope this helps, >>> >>> B >>> >>> (*) on Windows (currently) $HOME is $COOT_HOME which is the directory >>> WinCoot is installed in >>> >>> (x) wonder if this needs a better documentation, some can be found here: >>> >>> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Startup_files >>> >>> Hi recently found myself using coot on windows and was wondering where the user specific key bindings are to be introduced to coot. This was windows 7 and I think it defines the users home directory as C:\Users\user.name\ , but I know that other Windows versions use "C:\Documents and Settings\user.name" as the home. I tried to add my python coot bindings based off Bernhard Lohkamp to both of those locations and they didnt seem to get picked up. I then tried reading in the script bearing the key bindings using Calculate-Runscript- and picking the filename.py . Strangely that didnt work either. When I then copy-pasted the python script directly into the scripting window within coot using Calculate-Scripting-Python and then pasting in the code there. The key bindings did show up and work proving that there were no in-advertant syntax errors like new line charcaters etc that were corrupting the python syntax in the filename.py. Am I correct in that coot windows only supports python scripting and where do I have my key-bindings python scipt so that they are picked up on startup and show up in Extensions-Settings-Key-bindings. Thanks Hari >>> >>> >>> >>> >>> -- >>> *** >>> >>> Dr. Bernhard Lohkamp >>> Assistant Professor >>> Div. Molecular Structural Biology >>> Dept. of Medical Biochemistry and Biophysics (MBB) >>> Karolinska Institutet >>> S-17177 Stockholm >>> Sweden >>> >>> phone: (+46) 08-52487651 >>> fax: (+46) 08-327626 >>> email: bernhard.lohk...@ki.se > > > > -- > *** > > Dr. Bernhard Lohkamp > Assistant Professor > Div. Molecular Structural Biology > Dept. of Medical Biochemistry and Biophysics (MBB) > Karolinska Institutet > S-17177 Stockholm > Sweden > > phone: (+46) 08-52487651 > fax: (+46) 08-327626 > email: bernhard.lohk...@ki.se
Re: [COOT] Coot Book of the Genesis
...because the precompiled binary from the Coot site looks for some libraries it (and I) cannot find (see that January thread 'Help needed...' on the subject) and the suggestion there is to 'do it right and build from scratch'. But if you have another link to a RHEL binary I am happy to try again... Thx, BR -Original Message- From: Frank Thommen [mailto:structures...@embl-heidelberg.de] Sent: Thursday, February 09, 2012 1:17 AM To: COOT@JISCMAIL.AC.UK Cc: b...@hofkristallamt.org Subject: Re: Coot Book of the Genesis ...and why not simply use the binary RHEL 5 version? At least the CentOS 5 binary distribution works fine on CentOS 6. Why making one's life harder than needed? Cheers frank Frank Thommen - Structures IT Management and Support - EMBL Heidelberg structures...@embl-heidelberg.de - +49 6221 387 8353
Re: [COOT] Coot Book of the Genesis
...and why not simply use the binary RHEL 5 version? At least the CentOS 5 binary distribution works fine on CentOS 6. Why making one's life harder than needed? Cheers frank Bernhard Rupp (Hofkristallrat a.D.) wrote: Fellow Cooties, If it wasn't such a waste of time this would actually be funny: This installation on clean RHEL 6 turns out very much like the Book of Genesis: where Adam begets Seth who begets Enosh who begets Kenan who begets Mahalalel who begets Jared who eventually after a lot of fucking around begets Emsley who begets Coot: Coot_configure then begets Swig which begets Pcre which begets Glib which begets Zlib which begets Libffi which begets Gettext and after that bloodline is established by serious effing on my side, a little infidelity from Coot_configure then establishes a degenerate sideline by begetting mmdb, upon which in 2012 per Mayan calendar the Genesis apocalyptically ends in: checking if this is MINGW on Windows... no checking for MMDB... no Error locating necessary mmdb Ok we download and install checking for SSMLib... no! checking for Clipper... no! Error locating Clipper - a CNS-enabled version of Clipper (2.1-090520-ac or later) is required now maybe - just maybe - my own CNS which is already shutting down envisions that a functioning ccp4 installation should already be present? The major difference between my installing efforts and the Book actually is that per Genesis creation of the World took only 7 days... Best regards, BR PS: No more - zero please - bitching about Windows. Thank you. - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - No animals were hurt or killed during the production of this email. - -- Frank Thommen - Structures IT Management and Support - EMBL Heidelberg structures...@embl-heidelberg.de - +49 6221 387 8353
Re: [COOT] using custom key bindings in wincoot ( where to put .cootrc or equivalent in coot for windows)
Hi Hari, the file (in your $HOME) directory should be called .coot.py (dot-coot-dot-py). The dot in front is important (*)!!! coot.py is a very different file which is read in somewhere else. Alternatively put your coot.py file in the directory $HOME/.coot-preferences/ (again watch out for the dot!, in case the directory doesnt already exist). B (*) On Windows there may be the problem to rename it using the explorer. The DOS shell should allow you to do so. Hello Bernhard, Thanks for your email . It turns out that my file was not called coot.py and I also had a few "hidden" new-line characters due to a copy paste from your wiki python key bindings. Once I named the file coot.py and corrected the python syntax..I see the following behavior: At startup I do have windows coot inform me that it read in coot.py. However the key bindings do not work and do not show up in the User key bindings listing. Also activating a shortcut gives a "Key 119is not bound message" If I now read in the same coot.py using the Menu-Run-Script-select coot.py. The key-bindings then get registered and show up in the listing and work just great. So there is something..maybe in the order the python files are read in ..but having a valid coot.py file didnt add the key bindings at startup. I am wondering how I can avoid reading the key bindings in every time manually. Thanks Hari On Wed, Feb 8, 2012 at 2:57 AM, Bernhard Lohkamp wrote: Hi Hari, python scripts are read in from the following locations (*)(x): - $HOME/.coot.py (equivalent to .coot) - $HOME/.coot-preferences (a directory, all script file from here are read) - $COOT_PYTHON_EXTRAS_DIR (a directory which you can specify yourself) Calculate->Run script should always work. If it doesnt there may be something wrong with the script. What does the DOS console tell you. Hope this helps, B (*) on Windows (currently) $HOME is $COOT_HOME which is the directory WinCoot is installed in (x) wonder if this needs a better documentation, some can be found here: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Startup_files Hi recently found myself using coot on windows and was wondering where the user specific key bindings are to be introduced to coot. This was windows 7 and I think it defines the users home directory as C:\Users\user.name\ , but I know that other Windows versions use "C:\Documents and Settings\user.name" as the home. I tried to add my python coot bindings based off Bernhard Lohkamp to both of those locations and they didnt seem to get picked up. I then tried reading in the script bearing the key bindings using Calculate-Runscript- and picking the filename.py . Strangely that didnt work either. When I then copy-pasted the python script directly into the scripting window within coot using Calculate-Scripting-Python and then pasting in the code there. The key bindings did show up and work proving that there were no in-advertant syntax errors like new line charcaters etc that were corrupting the python syntax in the filename.py. Am I correct in that coot windows only supports python scripting and where do I have my key-bindings python scipt so that they are picked up on startup and show up in Extensions-Settings-Key-bindings. Thanks Hari -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
