Re: [COOT] CentOS 6 Screenshot
Is this really an X error, or can coot not find the executables for povray or raster3d? execlp [1] seems to complain that it can't find files, which may feed back to Guile Gtk that there is an error with a similar phenotype to an X error. [1] : http://unixhelp.ed.ac.uk/CGI/man-cgi?execlp+3 Are povray and raster3d in your $PATH? Just a thought. Mark On 7 Apr 2015, at 13:47, Bailey, Douglas (NIH/NCI) [E] baile...@mail.nih.gov wrote: Hello Everyone, When we run coot (0.8.2) on our CentOS 6_x64 systems and attempt DRAW=Screenshot=povray or raster3d we get an error similar to the following. We are using the latest build for CentOS 6_x64. The latest build for CentOS 5_x64 works fine on our CentOS 5 systems. Systems use the same NVIDIA graphics (K600) and driver version (340.32) CentOS 6_x64 error: ((safe_scheme_command) Error in proc: key: system-error args: (execlp ~A (No such file or directory) (2))) coot-bin: Fatal IO error 0 (Success) on X server :0.0. Gdk-ERROR **: The program 'coot-bin' received an X Window System error. This probably reflects a bug in the program. The error was 'BadGC (invalid GC parameter)'. (Details: serial 10420 error_code 13 request_code 60 minor_code 0) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) aborting... /home/dgb/coot/bin/coot: line 273: 28394 Aborted (core dumped) $coot_bin $@ ERROR: In procedure dynamic-link: ERROR: file: libguilegtk-2.0, message: file not found Any help, comments ideas would be appreciated. Thanks, Douglas Bailey NCI-Frederick 1050 Boyles Street Frederick, Maryland 21702 Ph: 301-846-5328 Fax: 301-846-6322 baile...@mail.nih.gov
Re: [COOT] Is there a way to dump the text from the command window in Windows7
Hi, A nice terminal program which has more features than the Windows cmd window (like easier copy and paste) is Console: http://sourceforge.net/projects/console/ The best version for me is this one: http://sourceforge.net/projects/console/files/console-devel/2.00/Console-2.00b147-Beta_32bit.zip/download (it's a beta, but the last stable release was in 2005, and the betas are still being released). Because I'm usually happier with unix style commands I then install cygwin, and get console to use the cygwin bash shell. Then you can redirect your standard output to a file: $superpose EOF superpose.log (superpose commands go here!) EOF The cygwin stuff is rather more involved and takes time to configure, but at least the Console program is an easy replacement for the windows cmd shell. Good luck. Mark On 13 February 2011 07:32, Jason Yano jky...@gmail.com wrote: Hi All, Is there an easy way to dump the text from the command window to a text file in Windows 7? I want to dump all of the information from SSM superpose into a text file. Currently there are 2 problems, 1) I can't select any of the text from the command window to copy it and 2) the window only scrolls so far. Any help would be great. Jason
Re: [COOT] Installation problems: Coot for OS X - from CCP4 / Fink
Hi, I'm not sure whether this is the problem, but have you updated X11 to a recent Xquartz release? (http://xquartz.macosforge.org/trac/wiki). IIRC the older ones gave problems. I hope this helps. Mark On 1 December 2010 10:41, Antony Oliver antony.oli...@sussex.ac.uk wrote: Dear all, I am trying to install the latest version of Coot on OS X. I have tried downloading the installer from CCP4, using Bill Scott's Fink pre-compiled binaries, and also using Fink to compile from source. Unfortunately every time I try to run Coot I get the same error... --- Wed Dec 1 10:37:24 coot-real[17558] Error: unknown error code: invalid pixel format Wed Dec 1 10:37:24 coot-real[17558] Error: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. The program 'coot-real' received an X Window System error. This probably reflects a bug in the program. The error was 'GLXBadContext'. (Details: serial 288 error_code 147 request_code 0 minor_code 3) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) --- Presumably there is a problem somewhere with one of the graphic library dependancies? Any help would be appreciated. Tony. = fink package is 0.6.2-pre-1-250 in the unstable tree of fink. = running OS X version 10.6.5 --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512
Re: [COOT] help with installing the latest version of coot
I'm getting this quite a lot too. Can you just install the packages with dpkg now? i.e. : dpkg -i /sw/fink/dists/unstable/main/binary-darwin-i386/sci/coot_0.6-pre-1-revision-2396-1_darwin-i386.deb dpkg -i /sw/fink/dists/unstable/main/binary-darwin-i386/sci/coot-shlibs_0.6-pre-1-revision-2396-1_darwin-i386.deb Mark 2009/10/8 KK katar...@mail.med.upenn.edu: Hi All, I am trying to install the latest version of coot on Mac 10.5.8 using fink and continue to get the following error: Errors were encountered while processing: /sw/fink/dists/unstable/main/binary-darwin-i386/sci/coot_0.6-pre-1-revision-2396- 1_darwin-i386.deb ### execution of /sw/bin/dpkg-lockwait failed, exit code 1 Failed: can't batch-install packages: /sw/fink/dists/unstable/main/binary-darwin- i386/sci/coot_0.6-pre-1-revision-2396-1_darwin-i386.deb /sw/fink/dists/unstable/main/binary-darwin-i386/sci/coot-shlibs_0.6-pre-1-revision-2396- 1_darwin-i386.deb Could anybody offer any suggestions as to what could I do to fix this issue? Thanks in advance KK -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay, France. Tel: (33) 169157968 Fax: (33) 169853715 Skype: markabrooks
Re: [COOT] problem with install on new Macbook Pro (OS X 10.5)
Hi, The CCP4 download page has a proper package, which works, despite being an older version. I had problems with his binaries too, (from this web page: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Installing_Coot_on_OS_X ) ...but the best way for me was to use his fink installation method (fink seems to be a wrapper for apt-get, as far as I can tell): http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled Synopsis: 1) Install fink 2) Edit /sw/etc/fink.conf 3) Update fink 4) Install Coot fink -b install coot ...which should give you a new binary: /sw/bin/coot This is a synopsis, but there are full instructions on the web page, starting here: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled#Before_you_begin I hope this helps Mark P.S. Thanks for the binaries Bill! 2009/6/5 Jason Greenwald jason.greenw...@phys.chem.ethz.ch: When I migrated to my new Macbook, COOT quit working properly. The icons/images do not appear for the majority of the GUI. I tried all three of the standalone binaries on Bill Scott's website. The only thing that works is the COOT app package from the CCP4 download site. However with the app package, I cannot have saved coot states for each directory that I work in. This same problem has been previously reported several times on this mail list but I could not find an answer. Lrge list of errors on startup and they start with: ** (coot-real:2205): WARNING **: Error loading pixmap file: /usr/local/xtal/coot/share/coot/pixmaps/display-manager.png Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-alt-conf.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-peptide-1.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/add-water.svg' Error loading icon: Couldn't recognize the image file format for file '/usr/local/xtal/coot/share/coot/pixmaps/anchor.svg' Any ideas? Thanks in advance, Jason -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay CEDEX. Tel: 0169157968 Fax: 0169853715 Skype: markabrooks
Re: [COOT] Coot 0.5.2 and Molprobity problem
Hi, The Phenix Molprobity binaries work for me on Coot 0.5 pre1 rev 1563 and 0.5 rev 1444. I can't say for Coot 5.2. I should do an update I guess, but I'm having a pause after CCP4 6.1, and Phenix 1.4.3. Updating Phenix also updates molprobity binaries too, which is handy: (define *probe-command* /usr/local/phenix/phenix-1.4- 3/build/intel-linux-2.6/bin/phenix.probe) (define *reduce-command* /usr/local/phenix/phenix-1.4-3/build/intel-linux-2.6/bin/phenix.reduce) These are the phenix versions, which work for me. probe.2.12.071128 reduce.3.14.080821 ...whereas these don't work and just give the blank windows and no pink clashes. probe.2.12.070727 reduce.3.10.080107 so be careful with the minor, minor version numbers! HTH, Mark 2009/1/7 Paul Emsley paul.ems...@bioch.ox.ac.uk Hi Ben, Ben Eisenbraun wrote: I seem to be running into the same problem reported by other people with Coot showing a blank clashes window. I'm using the official Coot 0.5.2 python-gtk2 binary on Fedora 10 with probe 2.12 and reduce 3.13. Probe/reduce seem to run correctly; I get a coot-molprobity output directory with files and their exit status is 0, but the dots are never drawn and the Molprobity Probe Clash Gaps window is blank with just a single OK button. I am using 2.12.071128 and that works fine on my Ubuntu machine. On my FC4 machine that causes an immediate crash. However, 2.12.070727 doesn't crash but behaves in the same manner as you describe. look at probe-dots.out. If you have (something like) :1-1:wc:A 6 VAL HG13 :A 92 ILE HA : that fails. If you have :1-1:wc: A 6 VAL HG13 : A 92 ILE HA : that works. Or so I think. If that is not the issue, then I don't know what it is. (The format change is to support hybrid_36 pdb files). An email in a similar thread from Bernhard Lohkamp on 11/18 suggested that if the window was blank, the version of probe was too old, but I don't see a more recent version. We encouraged them to make a new version for Windows. It would be nice if I could have a version that worked on FC4 too. Any clues on what I'm doing wrong would be much appreciated. HTH? See you soon, Paul. -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay CEDEX. Tel: 0169157968 Fax: 0169853715 Skype: markabrooks
Re: [COOT] problem in coot installation in ubuntu
Hi, I just tested it on a freshly installed system for a student; it works very well on Ubuntu Hardy. I'm not sure why nxnode is a dependency of the Coot .deb though! (Although that doesn't bother me too much- I would advise anyone to use NX ). Thanks again, Mark 2008/11/16 William G. Scott [EMAIL PROTECTED] That's great. In the short term, highly unofficial/unauthorized/zeroth-order coot and dependencies for i386 linux: debians: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files rpms (made via alien from above): http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Converting_to_rpm_packages These include mmdb, ssm, gpp4, fftw (in the form required for clipper and coot), clipper, coot, which will install into /usr/local/xtal and then the various guile-type dependencies, which will install into /usr On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote: FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on crystallographic libs for Ubuntu, e.g.: https://launchpad.net/ubuntu/+source/clipper https://launchpad.net/ubuntu/+source/mmdb When he gets round to Coot I'm keen to help make his life easier. Regards, Paul. Mark Brooks wrote: Hi, It may be useful to have a 'contrib' section for the Coot binary download web page (or even some unofficial web page), so that we have more options of binaries to test. For example, upon upgrading to Ubuntu Hardy Heron, Coot stopped working, for reasons beyond my understanding, but worked when recompiled. (Which was very easy using the build-it-gtk2-simple script BTW). To have a central repository of tested binaries could be very handy, to avoid having to do this. The Coot developers and yourself (Bill) have done an enormous amount to furnish us with working, tested programs, but perhaps one or two more updated binaries contributed by users would be useful, especially for newer releases of the myriad Linux flavours. I think for the Coot developers to start providing .deb, .rpm and Gentoo packages for every update is too onerous, especially when .tar.gz files work OK. Just my opinion. Which Ubuntu are you on Bill, and which binary are you using? Are these on your debian web site? I guess I may be able to give a Hardy Heron binary if need be. Thanks for your .debs though, I use them all the time. Mark 2008/11/12 William G. Scott [EMAIL PROTECTED] mailto: [EMAIL PROTECTED] Since Ubuntu has gotten to be popular (for good reason, IMO), it might be useful to have an official (or at least semi-official) debian package whose installation would guarantee all the dependencies also get installed. I've tried to do it in a half-arsed sort of way, but lately have dropped the ball (sorry). On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Hi! Firstly, do you need to build coot at all? There are binary packages which work just fine on Gutsy. You can install them wherever you want on your system, and they should just work. Secondly, if for some reason you do want to build your own (you want to make changes to the code???), then are you using the build-it-gtk2-simple script? http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code Building coot without this script requires days or weeks of messing around with dependencies. With this script it is usually pretty easy. Kevin Rimi wrote: Hi all, I am new to coot. Recently I tried to install coot in my ubuntu gutsy. But it can not find mmdb library somehow. Below is the message -- - William G. Scott contact info: http://chemistry.ucsc.edu/~wgscotthttp://chemistry.ucsc.edu/%7Ewgscott http://chemistry.ucsc.edu/%7Ewgscott Please reply to: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 Institut de Biochmie et de Biophysique Moleculaire et Cellulaire UMR8619 - Bât 430 - Université de Paris-Sud 91405 Orsay CEDEX Skype: markabrooks -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 Institut de Biochmie et de Biophysique Moleculaire et Cellulaire UMR8619 - Bât 430 - Université de Paris-Sud 91405 Orsay CEDEX Skype: markabrooks
Re: [COOT] Coot molprobity problem in Version 0.5?
Just a note to concur with this message. I'm getting this with 0.5, Ubuntu 8.04 32-bit. There was no problem with coot-0.5-pre-1-revision-1211 BTW. I haven't figured out why, and would love to know. Mark 2008/10/14 James M. Vergis [EMAIL PROTECTED] I think there is a problem with the way coot parses the output from coot-molprobity/probes-dots.out for displaying the probe clashes and making the Molprobity Probe Clash Gaps window. Using the reduce and probe versions in example #1 below, coot 0.5 will display the packing/clashes on the molecule but the Molprobity Probe Clash Gaps window where you can click on each residue doesn't display the information properly and will return a not found error and therefore not choose the residue. I think this is related to the extra space between the : and the A in the examples below. If I use the versions of reduce/probe that work fine in coot 0.4.1 in 0.5, the Molprobity Probe Clash Gaps window is empty and the clashes/packing are not drawn on the molecule. Running probe from the command line also results in these gaps(I hope all this makes sense). I have tried several combinations of reduce/probe (both compiled from source and downloaded binaries) and also tested this with a a pre-built binary to make sure my 64-bit version of coot 0.5 wasn't to blame. #1) PROBE-DOTS.OUT FROM VERSIONS OF REDUCE(3.03.070307)/PROBE(2.12.071128) MOSTLY WORK WITH COOT 0.5: [EMAIL PROTECTED] coot-molprobity]$ more probe-dots.out :1-1:wc: A 1 GLY C : A 2 ALA O :0.364:0.443:-23.028:17.043:-10.447:0.000:0.0027:C:O:-23.028:17.043:-10.447: 17.30:13.75 :1-1:wc: A 1 GLY C : A 2 ALA O :0.364:0.429:-22.911:17.044:-10.195:0.000:0.0033:C:O:-22.911:17.044:-10.195: 17.30:13.75 :1-1:wc: A 2 ALA C : A 1 GLY O :-0.001:0.297:-22.934:16.874:-10.243:0.000:0.0152:C:O:-22.934:16.874:-10.243 :12.50:19.32 :1-1:wc: A 2 ALA C : A 1 GLY O :-0.001:0.261:-22.605:16.482:-10.261:0.000:0.0211:C:O:-22.605:16.482:-10.261 :12.50:19.32 :1-1:wc: A 2 ALA C : A 1 GLY O :-0.001:0.340:-22.339:16.228:-10.136:0.000:0.0098:C:O:-22.339:16.228:-10.136 :12.50:19.32 #2) PROBE-DOTS.OUT FROM REDUCE(3.03.070307)/PROBE(2.12.070727) THAT WORK WITH COOT 0.4.1 BUT NOT 0.5: === [EMAIL PROTECTED] bin]$ more coot-molprobity/probe-dots.out :1-1:wc:A 1 GLY C :A 2 ALA O :0.364:0.443:-23.028:17.043:-10.447:0.000:0.0027:C:O:-23.028:17.043:-10.447: 17.30:13.75 :1-1:wc:A 1 GLY C :A 2 ALA O :0.364:0.429:-22.911:17.044:-10.195:0.000:0.0033:C:O:-22.911:17.044:-10.195: 17.30:13.75 :1-1:wc:A 2 ALA C :A 1 GLY O :-0.001:0.297:-22.934:16.874:-10.243:0.000:0.0152:C:O:-22.934:16.874:-10.243 :12.50:19.32 :1-1:wc:A 2 ALA C :A 1 GLY O :-0.001:0.261:-22.605:16.482:-10.261:0.000:0.0211:C:O:-22.605:16.482:-10.261 :12.50:19.32 :1-1:wc:A 2 ALA C :A 1 GLY O :-0.001:0.340:-22.339:16.228:-10.136:0.000:0.0098:C:O:-22.339:16.228:-10.136 :12.50:19.32 James M. Vergis, Ph.D. University of Virginia Molecular Physiology and Biological Physics MKWEINR 360A Snyder Building 480 Ray C. Hunt Drive PO Box 800886 Charlottesville, VA 22908-0886 phone: 434-243-2730 FAX: 434-243-8271 [EMAIL PROTECTED] -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 Institut de Biochmie et de Biophysique Moleculaire et Cellulaire UMR8619 - Bât 430 - Université de Paris-Sud 91405 Orsay CEDEX
