Re: [COOT] coot 0.9.4.1 installation on centos 8
Sorry, I am still struggling to get it working on Ubuntu and on os x. > On Feb 28, 2021, at 6:42 AM, Ming Sun wrote: > > Hi Bill and Paul > > Thanks for the messages. However, I tried removing the reducent libpng files > in the coot bin lib folder, and also tried several other different Scientific > Linux versions of coot. However, it is still not working. I'm wondering if > it's more of a cenos8 issue in general or some other local set-up. > > Any suggestions are warmly welcomed. Thank you all again. > > best, > Ming > > On Mon, Feb 22, 2021 at 11:18 AM William G. Scott wrote: > Hi Ming: > > I got some similar errors on my Ubuntu install. Removing some of the > non-coot libraries (like libpng) that are duplicated might help. Also, make > sure you have the appropriate processor architecture. > > Bill > > > > > On Feb 22, 2021, at 8:14 AM, Ming Sun wrote: > > > > Hi all > > > > I'm trying to install the recent released version of coot on centos 8 linux > > machine. However, I keep having the following error messages. Any inputs > > are warmly welcome. Many thanks in advances > > > > coot version, > > coot-0.9.4.1-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz, > > released on 2021-02-02 > > > > error messages: > > /home/software/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/libexec/coot-bin: > > error while loading shared libraries: libpng15.so.15: wrong ELF class: > > ELFCLASS32 > > > > create soft link in coot/lib/ but not working either > > sudo ln -s /bin/lib/libpng15.so.15 > > coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libpng15.so.15 > > > > Thanks! > > Ming > > > > > > > > To unsubscribe from the COOT list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > > > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing > > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > > https://www.jiscmail.ac.uk/policyandsecurity/ > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] coot 0.9.4.1 installation on centos 8
Hi Ming: I got some similar errors on my Ubuntu install. Removing some of the non-coot libraries (like libpng) that are duplicated might help. Also, make sure you have the appropriate processor architecture. Bill > On Feb 22, 2021, at 8:14 AM, Ming Sun wrote: > > Hi all > > I'm trying to install the recent released version of coot on centos 8 linux > machine. However, I keep having the following error messages. Any inputs are > warmly welcome. Many thanks in advances > > coot version, > coot-0.9.4.1-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.tar.gz, > released on 2021-02-02 > > error messages: > /home/software/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/libexec/coot-bin: > error while loading shared libraries: libpng15.so.15: wrong ELF class: > ELFCLASS32 > > create soft link in coot/lib/ but not working either > sudo ln -s /bin/lib/libpng15.so.15 > coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libpng15.so.15 > > Thanks! > Ming > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list > hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] latest osx version of coot
Hi Leonard et al: I want to apologize to you and everyone for dropping the ball on this. Between a massive wildfire that almost took out our house (and destroyed those of several colleagues), the pandemic, a forced lab move on short notice, and a pile of new teaching assignments, I haven’t managed to put some time into this for awhile. I’ll try to do so as soon as I can. Meanwhile, a CCP4 update might be the best bet. Sorry. Bill > On Nov 11, 2020, at 7:57 AM, Thomas, Leonard M. wrote: > > Okay after trolling the wiki and other site I cannot find anything about the > latest version of COOT for OSX. > > Any pointers would be grateful. > > Len Thomas > > Leonard M. Thomas Ph.D. > Macromolecular Crystallography Laboratory > Department of Chemistry and Biochemistry > University of Oklahoma > 101 Stephenson Parkway > Norman, OK 73019 > 405-325-1126 > lmtho...@ou.edu > http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list > hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] Coot Fink 10.15
Hi Ed: I invested a lot of time into fink, so I was reluctant to let it go, but it might be time. When it was at its prime, it was the best-managed and and most science-oriented of the third-party package manager systems. MacPorts is another option I want to take a look at. To be honest, I kind of have burned out on this stuff in the last few years. We will figure something out. Compared to all that is going on in NYC right now, these problems will hopefully be minor. Take care. Bill William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/SARS-CoV-2/ > On Apr 24, 2020, at 7:35 PM, Edward Miller wrote: > > Thanks, Bill, as always for the dedicated support. > > I've been a fink user, actually due to your packages, for at least ten years. > > Maybe it's time to switch to home-brew? Would they have more gtk+2 > flexibility? > > Best, > > Ed Miller > > On Fri, Apr 24, 2020 at 4:52 PM William G. Scott wrote: > Hi Ed (and COOT list): > > I’ve put updated info files here: http://scottlab.ucsc.edu/fink/finkupdate/ > > I’m trying to get these into fink as soon as possible, BUT there are two > show-stopper problems: > > (1) The old refmac I have won’t compile with the newer versions of gcc, and > we really need a new version of this anyway for coot. (Coot only requires > refmac at runtime, so it can use whatever version you might have with CCP4). > If anyone knows of a more recent version that is available for unrestricted > download and installation, please let me know. > > (2) Coot itself requires a newer version of gtk+2 than what fink has, and > they are objecting that the newer version of gtk+2 has bugs in it that break > other programs, so I am stuck on a pre-release version of coot. > > None of this is at all satisfactory, and I apologize. > > I haven’t yet had a chance to download the most recent CCP4 package, but from > what I understand, it has the latest coot (and refmac), so if you need the > new version, I suggest you do that. > > > If we can’t have a more recent version of coot in fink vs. ccp4, and can’t > have refmac, it kind of makes it pointless to maintain coot in fink. > > Bill > > William G. Scott > Director, Program in Biochemistry and Molecular Biology > Professor, Department of Chemistry and Biochemistry > and The Center for the Molecular Biology of RNA > University of California at Santa Cruz > Santa Cruz, California 95064 > USA > > > > > On Apr 24, 2020, at 10:24 AM, William G. Scott wrote: > > > > Hi Ed: > > > > Briefly, I need to update the package. > > > > Less briefly, I need to change to gcc9, which is easy, and I need to update > > to the latest version of coot, 0.9, which is proving to be a nightmare. > > > > I need to go teach a class and will then get back to you with something I > > hope will work. > > > > Bill > > > > PS: If you just want the latest coot, it looks like the latest version of > > CCP4, just released, has it. They are ahead of me. > > > > > > > > > > William G. Scott > > Director, Program in Biochemistry and Molecular Biology > > Professor, Department of Chemistry and Biochemistry > > and The Center for the Molecular Biology of RNA > > University of California at Santa Cruz > > Santa Cruz, California 95064 > > USA > > > > > > > >> On Apr 24, 2020, at 8:57 AM, Edward Miller wrote: > >> > >> Hi Professor Scott, > >> > >> I'm trying to install coot via fink on OS X 10.15. This is a clean fink > >> install, so I completely blasted my /sw directory prior to this. > >> > >> The installation is looking for a gcc5 package: > >> > >> Can't resolve dependency "gcc5-shlibs (>= 5.1.0-2)" for package > >> "coot-0.8.9-2" (no matching packages/versions found) > >> Exiting with failure. > >> > >> Is this dependency correct? > >> > >> Thanks for your help and for contributing to crystallography on os x for > >> all these years. > >> > >> Ed Miller > > > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
Re: [COOT] Coot Fink 10.15
Hi Ed (and COOT list): I’ve put updated info files here: http://scottlab.ucsc.edu/fink/finkupdate/ I’m trying to get these into fink as soon as possible, BUT there are two show-stopper problems: (1) The old refmac I have won’t compile with the newer versions of gcc, and we really need a new version of this anyway for coot. (Coot only requires refmac at runtime, so it can use whatever version you might have with CCP4). If anyone knows of a more recent version that is available for unrestricted download and installation, please let me know. (2) Coot itself requires a newer version of gtk+2 than what fink has, and they are objecting that the newer version of gtk+2 has bugs in it that break other programs, so I am stuck on a pre-release version of coot. None of this is at all satisfactory, and I apologize. I haven’t yet had a chance to download the most recent CCP4 package, but from what I understand, it has the latest coot (and refmac), so if you need the new version, I suggest you do that. If we can’t have a more recent version of coot in fink vs. ccp4, and can’t have refmac, it kind of makes it pointless to maintain coot in fink. Bill William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA > On Apr 24, 2020, at 10:24 AM, William G. Scott wrote: > > Hi Ed: > > Briefly, I need to update the package. > > Less briefly, I need to change to gcc9, which is easy, and I need to update > to the latest version of coot, 0.9, which is proving to be a nightmare. > > I need to go teach a class and will then get back to you with something I > hope will work. > > Bill > > PS: If you just want the latest coot, it looks like the latest version of > CCP4, just released, has it. They are ahead of me. > > > > > William G. Scott > Director, Program in Biochemistry and Molecular Biology > Professor, Department of Chemistry and Biochemistry > and The Center for the Molecular Biology of RNA > University of California at Santa Cruz > Santa Cruz, California 95064 > USA > > > >> On Apr 24, 2020, at 8:57 AM, Edward Miller wrote: >> >> Hi Professor Scott, >> >> I'm trying to install coot via fink on OS X 10.15. This is a clean fink >> install, so I completely blasted my /sw directory prior to this. >> >> The installation is looking for a gcc5 package: >> >> Can't resolve dependency "gcc5-shlibs (>= 5.1.0-2)" for package >> "coot-0.8.9-2" (no matching packages/versions found) >> Exiting with failure. >> >> Is this dependency correct? >> >> Thanks for your help and for contributing to crystallography on os x for all >> these years. >> >> Ed Miller > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
Re: [COOT] error No appropriate OpenGL-capable visual found
Try re-installing Xquartz. https://www.xquartz.org William G. Scott http://scottlab.ucsc.edu > On Apr 4, 2018, at 4:52 PM, Elena Zehr <zehr.el...@gmail.com> wrote: > > Hi, > > After upgrading my MacOS to High Sierra, coot stopped running giving me the > error below. Do you know what is missing? > > bash-3.2$ coot > INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: > /programs/i386-mac/ccp4/7.0/ccp4-7.0/lib/data/monomers/ > INFO:: Reading coordinate file: > /programs/i386-mac/ccp4/7.0/ccp4-7.0/share/coot/standard-residues.pdb > PDB file > /programs/i386-mac/ccp4/7.0/ccp4-7.0/share/coot/standard-residues.pdb has > been read. > Spacegroup: P 1 > > *** Cannot find the double-buffered visual. > *** Trying single-buffered visual. > > *** No appropriate OpenGL-capable visual found. > catching the crash log: > coot-exe: "/programs/i386-mac/ccp4/7.0/ccp4-7.0/libexec/coot-bin" > coot-version: > /programs/i386-mac/ccp4/7.0/ccp4-7.0/libexec/coot-bin > platform: > /usr/bin/uname > core: #f > No core file found. No debugging > > > Many thanks, > Elena
Re: [COOT] Mac Binaries (Release 0.8.9.1)
For those using fink, I’ve updated the fink package info file http://fennario.ucsc.edu/~wgscott/coot/finkinfo/coot.info I still need to figure out how to get it into fink. Meanwhile, you can put the file in /sw/fink/dists/stable/main/finkinfo/sci and build it. William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu > On Apr 1, 2018, at 10:58 PM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > On 01/04/2018 22:00, Paul Emsley wrote: >> We are pleased to announce the 14th Anniversary release of Coot: 0.8.9.1 > > Mac binaries: > > http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/ > > Thanks Bill. > > Paul.
[COOT] New hardware lets any computer run an interactive, 3D interface | Ars Technica
I wonder if coot might be able to take advantage of this: > https://arstechnica.com/science/2017/11/new-hardware-lets-any-computer-run-an-interactive-3d-interface/ > > <https://arstechnica.com/science/2017/11/new-hardware-lets-any-computer-run-an-interactive-3d-interface/> William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu
Re: [COOT] APBS binary location MacPymol
On Oct 27, 2014, at 5:48 AM, Lau Sze Yi lau_sze...@immunol.a-star.edu.sg wrote: Hi, I had MacPyMOL. In order to use APBS, I rename app to MacPyMOLX11Hybrid. I am ask to supply the APBS binary location but could not find it. Regards, Sze Yi You have to install it separately. You might get better responses asking about pymol on the pymol mailing list. (Asking questions about PyMOL on the coot email list is kind of like ordering flowers for your mistress on your spouse’s cell phone and credit card.) William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA
Re: [COOT] Stand Alone Coot for 10.6–10.8
Sorry. I forgot to change one occurrence in the build script. Should be fixed now. William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/~wgscott On Sep 18, 2014, at 6:12 PM, Mark A Saper sa...@umich.edu wrote: Hi Bill, I installed the latest stand alone Coot from the 10.6 page and the file /Library/Coot/bin/coot-bin does not exist. Any idea where it is? Thanks, Mark ___ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School 3040 Chemistry Building | sa...@umich.edu | +1 (734) 764-3353
[COOT] Coot on OS X 10.6.X ?
Hi folks: Does anyone use my pre-compiled version of coot for OS X 10.6 anymore? (This would be either the 10.6 stand-alone or the fink debian distribution)? Fink has discontinued support for 10.6, and I only have the one mac mini in my lab running it, so at some point the end is inevitable. (My personal, irrelevant opinion was that 10.6.8 was the best version of OS X and it has been in decline ever since.) Also, we made a lot of small changes recently in the 10.7-10.9 coot fink dist and the 10.9 stand-alone packages, so please let me know if there is any weirdness. All the best, Bill William G. Scott http://scottlab.ucsc.edu/~wgscott
Re: [COOT] Extensions Menu disappeared
Another option is to install this manually: curl -O http://fennario.ucsc.edu/fink_intel_10.9_64bit_sw/10.9/local/main/binary-darwin-x86_64/guile18-gtk-shlibs_2.1-1_darwin-x86_64.deb” curl -O “http://fennario.ucsc.edu/fink_intel_10.9_64bit_sw/10.9/local/main/binary-darwin-x86_64/guile18-gtk_2.1-1_darwin-x86_64.deb” sudo dpkg -i *.deb This is the same package with a later epoch label so fink updates won’t touch it. On Sep 3, 2014, at 10:40 AM, William G. Scott wgsc...@ucsc.edu wrote: On Sep 3, 2014, at 5:33 AM, Dimitry Rodionov d.rodio...@gmail.com wrote: Hi Jianghai, Building Coot from source using fink solved this problem for me. Regards, Dmitry On Sep 3, 2014 8:22 AM, Jianghai Zhu z...@crystal.harvard.edu wrote: Hi all, I am using Coot 0.8-pre-revision-5201-1 under OS X 10.9.4. I installed it using Bill’s fink binary. Now when I ran Coot, the Extensions Menu disappeared. I got the following error during the start of Coot. load coot-gui.scm” (Error in proc: unbound-variable args: (#f Unbound variable: ~S (gtk-callback-trampoline) #f)) When I ran Coot from PHENIX package, the Extensions Menu also disappeared. Could anyone give me some suggestions on how to resolve this issue? Thanks a lot. — Jianghai I ran into this kind of thing before, and it turned out to be bug in the guile18-gtk-shlibs debian file that fink distributed (rather than mine). It can be a wee bit finicky. Try re-compiling guile18-gtk At some point we hope to remove this as a dependency. Sorry. Bill
[COOT] symmetry operator notation question
Hi folks:
What is the meaning of the last field — the one in curly brackets -- that
describes the symmetry transformation of a given atom in coot? For example, for
a given X Y Z, coot displays the symmetry transformation of an equivalent
position as Y+1/2, -X+1/2, Z + (0 -1 1) { 1 0 1 }”.
Thanks.
Bill
William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http://scottlab.ucsc.edu/~wgscott
Re: [COOT] r5166 python error on Mac
Dear Oliver et al: On Jul 20, 2014, at 8:54 AM, Oliver Clarke oc2...@columbia.edu wrote: WARNING:: No coot.py file found! Python scripting unavailable. It looks like this is the problem. For some reason it is no longer getting copied from the src to python directory. If I do this manually, it works. I’m working on update/fix now. I apologize for not seeing this on July 20th. Bill
Re: [COOT] coot crash when loading mtz file
On Jun 19, 2014, at 9:33 AM, William G. Scott wgsc...@ucsc.edu wrote: If the user has set $DYLD_LIBRARY_PATH (perhaps via ccp4), it is possible this gets over-ridden. I can reproducibly mess coot up with this: export DYLD_LIBRARY_PATH=/Applications/ccp4-6.4.0/lib and un-mess it up with this: export DYLD_LIBRARY_PATH=
Re: [COOT] unable to launch coot
Dear Nacho: The “coot-pre” package should work. In updating that, I think I probably broke the “stable” coot package. Also, the stand-alone ones all work (just tested). http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot Sorry, Bill On Mar 14, 2014, at 10:23 AM, Ignacio Mir Sanchis imirsanc...@uchicago.edu wrote: Dear cooters, I installed fink and packages (in OS X 10.9.2) following directions from Scott lab web page (http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up) When I try to launch coot this message appears: dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_ Referenced from: /sw/lib/libcoot-lidia-core.0.dylib Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib in /sw/lib/libcoot-lidia-core.0.dylib /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real $@ Can anyone tell me what I'm doing wrong? Thank you so much in advance. Nacho William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/scottlab/
Re: [COOT] unable to launch coot
I am updating the “stable” coot in fink to rev. 4965 which should work fine with the latest rkdit. On Mar 14, 2014, at 11:11 AM, William G. Scott wgsc...@ucsc.edu wrote: Dear Nacho: The “coot-pre” package should work. In updating that, I think I probably broke the “stable” coot package. Also, the stand-alone ones all work (just tested). http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot Sorry, Bill On Mar 14, 2014, at 10:23 AM, Ignacio Mir Sanchis imirsanc...@uchicago.edu wrote: Dear cooters, I installed fink and packages (in OS X 10.9.2) following directions from Scott lab web page (http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up) When I try to launch coot this message appears: dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_ Referenced from: /sw/lib/libcoot-lidia-core.0.dylib Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib in /sw/lib/libcoot-lidia-core.0.dylib /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real $@ Can anyone tell me what I'm doing wrong? Thank you so much in advance. Nacho William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/scottlab/
Re: [COOT] coot - save coordinates
I am clueless on this one, so I'll post it to the coot mailing list in case anyone else has seen this …. On Oct 8, 2013, at 9:53 PM, Felix Frolow wrote: Hi Bill, I regularly update coot using FINK ( from your repository) Since one of the recent versions of coot ( difficult to say from when, maybe couple of month back) save of coordinates take unreasonably long time. Simultaneously a flowing message appears: INFO:: Setting fileselection with file: /Users/mbfrolow/ModificationOfM_refmac1-coot-0.pdb (filter-fileselection-filenames-state) sys:1: GtkWarning: Unable to find default local directory monitor type Fontconfig warning: ignoring UTF-8: not a valid region tag sys:1: GtkWarning: Could not find the icon 'application-x-palm-database'. The 'hicolor' theme was not found either, perhaps you need to install it. You can get a copy from: http://icon-theme.freedesktop.org/releases Could you please comment? I use MacBook Pro with Mountain Lion which is probably which I guess is irrelevant. Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor
Re: [COOT] Symbol not found: _iconv
On Sep 20, 2013, at 6:54 AM, Daniele de Sanctis de.sanct...@gmail.com wrote: I already tried everything I found on the web (Reinstall OS, Repair disk etc). Thanks in advance for your help Daniele Hi Daniele: This is usually due to setting $DYLD_LIBRARY_PATH which is best avoided. I think the ccp4 shell initialization scripts do this still. If /Applications/coot.app requires that, it is broken. Before doing anything radical like reinstalling OS X, unsetting $DYLD_LIBRARY_PATH is at least worth a try, i.e., export DYLD_LIBRARY_PATH= on bash or zsh, or unsetenv DYLD_LIBRARY_PATH on tcsh should do it. Also, you could try installing coot from here, as a control (or an alternative): http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot Good luck. 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
Re: [COOT] fink: coot-0.7.1.0-6 for 10.6
On Sep 5, 2013, at 3:43 AM, Steffen Schmidt steffen.schm...@tuebingen.mpg.de wrote: coot0.7.1.0-7 Crystallographic molecular graphics coot-pre0.8-pre-4749Crystallographic molecular graphics refmac 5.7.0032-3 CCP4 refmac5 standalone update Great, it works for me also! Do you plan to have it also available for 10.6? Done!
Re: [COOT] fink: coot-0.7.1.0-6 - refmac cif file not found
On Sep 5, 2013, at 3:43 AM, Steffen Schmidt steffen.schm...@tuebingen.mpg.de wrote: OK, I fixed it properly now. (I hope). The newest revisions for coot, refmac and coot-pre are these: coot0.7.1.0-7 Crystallographic molecular graphics coot-pre0.8-pre-4749Crystallographic molecular graphics refmac 5.7.0032-3 CCP4 refmac5 standalone update Great, it works for me also! Do you plan to have it also available for 10.6? Steffen Yes, I'll try to get it done (tested) today. 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
Re: [COOT] fink: coot-0.7.1.0-6 - refmac cif file not found
On Sep 4, 2013, at 7:42 AM, Steffen Schmidt steffen.schm...@tuebingen.mpg.de wrote: Hey Bill, I noticed that coot complains that WARNING: in init_refmac_mon_lib file /sw/share/coot/lib/data/monomers/list/mon_lib_list.cif not found. WARNING:: energy lib /sw/share/coot/lib/data/monomers/ener_lib.cif not found. It looks like you can fix this by changing /sw/share/coot/lib/data/monomers to a symlink to refmac: ln -s /sw/share/refmac/monomers /sw/share/coot/lib/data/ Are the soft link that you create in the .info file correct for you? Best Steffen OK, I fixed it properly now. (I hope). The newest revisions for coot, refmac and coot-pre are these: coot0.7.1.0-7 Crystallographic molecular graphics coot-pre0.8-pre-4749Crystallographic molecular graphics refmac 5.7.0032-3 CCP4 refmac5 standalone update
Re: [COOT] Downloading Coot
On Sep 3, 2013, at 1:04 PM, Dale Tronrud det...@uoxray.uoregon.edu wrote: I was looking for the download site for Coot but the links have have found point to http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ but there is nothing there. Where do I go to find prebuilt coot binaries? Dale Tronrud Paul's binaries are here: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/ OS X ones I built are here: http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot Source code is here: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/ Windows version is here: http://www.ysbl.york.ac.uk/~lohkamp/coot/
[COOT] maintaining Coot on OS 10.6.8
On Apr 24, 2013, at 1:40 AM, Andreas Förster docandr...@gmail.com wrote: Dear Özkan and all, this question was asked by Dave a month and a half ago (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1303L=cootP=R286), but there was no reply. Snow Leopard is deprecated, even though 25% of OSX users, presumably unwilling to downgrade their laptop to a smartphone clone, still use it. I understand that Bill doesn't have an SL machine anymore. But please, please, is there a way to keep coot going on SL? Andreas HI Andreas: I have two machines running 10.6.8, and as long as one of those is still alive, I still plan to maintain this. I don't have 10.7, and will probably update 10.8 to 10.9 when the time comes (unless they botch it as much as they did 10.7). Sorry about not answering the questions earlier. I've been trying to rehab from a broken ankle and so am even a bit more out of it than usual. Bill
Re: [COOT] Latest Coot from Fink crashing
Sorry. I just got my 10.6 computer back up and did another build a few hours ago. I haven't been able to reproduce the issue, but was only trying on 10.8. I'm having python mis-match problems on 10.6. On Feb 19, 2013, at 7:21 PM, Dmitry Rodionov d.rodio...@gmail.com wrote: This seems to be a 10.6 issue since same version on 10.8 centres fine. On 2013-02-19, at 4:09 PM, Dmitry Rodionov d.rodio...@gmail.com wrote: Dear all, After upgrading to latest (Fink's 0.7.1-pre-4562) coot we are experiencing a strange problem: coot reproducibly crashes if one tries to centre on a non-protein non-water atom. Coot's last words: (0) S /1/chainid=B/1/DMS, occ: 0.79 with B-factor: 27.78 element: S at (12.282,65.946,153.1) : 0.180006 INFO:: recentre: clicked on imol: 0 coot-real(60501,0x7fff71290cc0) malloc: *** error for object 0x7fff5fbfbd68: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug /sw/bin/coot: line 6: 60501 Abort trap /sw/bin/coot-real $@ or (0) P /1/chainid=/1/PO4, occ: 1 with B-factor: 30 element: P at (0,0.021,0.036) : 0.153325 INFO:: recentre: clicked on imol: 0 coot-real(19455,0x7fff70f8dcc0) malloc: *** error for object 0x7fff5fbfbea8: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug /sw/bin/coot: line 6: 19455 Abort trap /sw/bin/coot-real $@ every time it's something about pointer being freed was not allocated. Purging and rebuilding Coot does not fix the problem. Has anybody seen this behaviour? Best regards, Dmitry
[COOT] New pre-release for 10.8 with rdkit
Hi Citizens: I've tried to put together a new coot package with rdkit incorporated. I would be grateful if anyone would be willing to test it on OS X 10.8.2. You can get it here: http://psbmini.ucsc.edu/~wgscott/coot/?C=M;O=D or using apt-get in fink. I tried compiling it on 10.6.8 and crashed my computer with the main website on it. Sorry. I can't drive due to a broken ankle so it might be awhile before it is up again. Good luck. 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
Re: [COOT] coot crushes in the beginning
On Feb 8, 2013, at 3:29 PM, Arto artop...@berkeley.edu wrote: /Users/pulk/.coot-preferences/0-coot-history.scm Try moving or deleting that file and see if it works again.
[COOT] next version?
Which button in COOT do I press to print a PDB file represented as a ball-and-stick model to get a 3D printout from someplace like this? http://www.shapeways.com 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
Re: [COOT] No updates
Paul has worked his arse off for over 10 years on Coot, and has made it free, as in beer, for us, and very deservingly has now got a job at the best place on the planet to do science. Maybe this is a good time for us all to say thanks and congratulations, to cheer him on, and to give him a chance to unpack. -- 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 On Nov 12, 2012, at 12:25 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: On Sat, 2012-11-10 at 16:08 +0100, Jon Agirre wrote: Starting in October, I noticed that Paul changed his e-mail address from ox.ac.uk to cam.ac.uk. I wonder if it has anything to do with the lack of updates. Yes. Everything (actually MRC-LMB (and what that has to do with cam.ac.uk I have no idea)). The Oxford site is dead for all practical purposes (I can no longer log in to change things). I will try to get a new permanent home on the web for Coot - when that's in place, I will let you know. Cheers, Paul.
Re: [COOT] Release 0.7
Additional OS X builds are linked here: http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot On Sep 29, 2012, at 2:49 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: Mac 10.8: http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/Coot-0.7-stable_64bit_10.8.2.pkg.zip
Re: [COOT] fink stuff (OS X)
On Sep 7, 2012, at 2:38 AM, Chris Richardson chris.richard...@icr.ac.uk wrote: Apologies for reanimating this long-dead discussion, but did you reach a conclusion about putting ccp4 6.3.0 in fink? Apologies to everyone for the delay. Yes. I'm now posting news about fink updates relevant to coot and ccp4 here: http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Crystallography_on_OSX_Blog I hope this will be of use to someone. You can post comments, suggestions, job offers and death threats without impediment. Ultimately I am hoping to have a separate ccp4-libs package that can be used for coot and the ccp4 suite, to prevent users from having to install two sets of what should be the same libraries. Peace and joy, 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
Re: [COOT] 0.7-pre-1-4305 crashes on OSX 10.8
This is my fault. The problem is caused by line #5 in the /sw/bin/coot wrapper script. Instead of export PYTHONPATH=/sw/lib/python2.7/site-packages:/sw/lib/python2.7/site-packages/gtk-2.0:/sw/share/coot/python:$PYTHONPATH try export PYTHONPATH=/sw/lib/python2.7/site-packages:/sw/lib/python2.7/site-packages/gtk-2.0:/sw/share/coot/python and it should work. Coot is inheriting $PYTHONPATH from some other location, probably CCP4, and is getting messed up. I'm about to update the fink package, as soon as I confirm today's svn (r4386) compiles and behaves. Sorry. 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) email: wgsc...@ucsc.edu On Sep 4, 2012, at 5:38 AM, Martin Montgomery m...@mrc-mbu.cam.ac.uk wrote: If you feel like testing, please copy over the following python files from your 4303 to 4305 installation: python/user-defined-restraints.py python/coot-utils.py python/extension.py fingers crossed that should help. Thanks Paul, However, I copied over the python files from 4303 (I don't have a user_defined_restraints.py) and still get the error. Fatal Python error: PyThreadState_Get: no current thread /sw/bin/coot: line 6: 37821 Abort trap: 6 /sw/bin/coot-real $@ Regards MGM On 4 Sep 2012, at 12:22, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: On 04/09/12 10:23, Martin Montgomery wrote: Hello, I'm having trouble with 0.7-pre-1-4305 installed through fink on osx 10.8.1 I updated to fink 0.34.3 then coot 0.7-pre-1-4305. Coot now crashes after the launch of the splash screen with the following message: Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) DEBUG:: stating pydirectory /sw/share/coot/python INFO:: importing coot.py from /sw/share/coot/python/coot.py Importing python module coot using command from coot import * INFO:: coot.py imported Fatal Python error: PyThreadState_Get: no current thread /sw/bin/coot: line 6: 50934 Abort trap: 6 /sw/bin/coot-real $@ The previous version (4303) was working perfectly (and still is on my laptop with fink 0.34.2). A quick google showed at least two others had found the same problem but hadn't posted to the list. Is there a fix? I didn't know about this recent problem until I (too) did some googling. I did see a ChangeLog entry from 2004: * src/main.cc (main): Put PYTHON macroed code before GUILE, so that python is initialized when we have --with-guile --with-python, which deals with Fatal Python error: PyThreadState_Get: no current thread. which makes me believe that I have inadvertently somehow made a similar mistake (that is only apparent on Mac XXX). How I could have done that and why it only fails on Mac, I don't know. Having said that, if you have localized the problem between 4303 and 4305 (as seems to be the case), Bernhard (who is now on holiday) wrote r4304 and r4305 - but that consists mostly of python scripting changes (the prosmart interface, in particular). If you feel like testing, please copy over the following python files from your 4303 to 4305 installation: python/user-defined-restraints.py python/coot-utils.py python/extension.py fingers crossed that should help. Paul.
Re: [COOT] problem with Auto open MTZ in coot
What happens if you try to display a pdb and map downloaded from the EDS? I believe that uses the same auto-open sequence, and it would help in figuring out whether the problem is with a refmac incompatibility or something else… On Aug 2, 2012, at 8:13 AM, Pernigo, Stefano stefano.1.pern...@kcl.ac.uk wrote: Dear coot users, I've tried to auto-open several MTZ files without success.
Re: [COOT] CCP4 6.3.0 released
On Jul 17, 2012, at 6:25 AM, Felix Frolow wrote: I will wait for fink version if it will be one… :-\ Does anyone use or want this anymore? -- 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) email:wgsc...@ucsc.edu
Re: [COOT] CCP4 6.3.0 released
I don't, but I will try to get it done by the time 10.8 is released, if not sooner. 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) email:wgsc...@ucsc.edu On Jul 17, 2012, at 2:53 PM, jbosch wrote: Bill I insist, I'm completely finked. And if you can have a 10.8 pre-release that would be great too. Jürgen On Jul 17, 2012, at 5:34 PM, William G. Scott wrote: On Jul 17, 2012, at 6:25 AM, Felix Frolow wrote: I will wait for fink version if it will be one… :-\ Does anyone use or want this anymore? -- 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) email:wgsc...@ucsc.edu
Re: [COOT] Coot nucleic acid issue
The executable coot is really a wrapper shell script for coot-real, which is the coot binary. The shell script in essence sets up the environment in which coot runs. The relevant variable for finding the coot refmac dictionary (library) directory is called $COOT_REFMAC_LIB_DIR Where these point to will be different for different installations. For my OS X pre-built coot, it looks like this: cat /usr/local/bin/coot #!/bin/sh -f source /Library/Coot/bin/init.sh export COOT_REFMAC_LIB_DIR=/Library/Coot/share/coot/lib export COOT_PYTHON_DIR=/Library/Coot/share/coot/python export COOT_SBASE_DIR=$CCP4/share/sbase export PYTHONPATH=/Library/Coot/lib/python2.7/site-packages:/Library/Coot/lib/python2.7/site-packages/gtk-2.0:/Library/Coot/share/coot/python:$PYTHONPATH /Library/Coot/bin/coot-real $@ 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) email: wgsc...@ucsc.edu On Mar 29, 2012, at 8:55 AM, Longfei Wang wrote: Hi William, Thank you for your suggestion. Another question, how to import the whole dictionary into coot? Best Longfei On Tue, Mar 27, 2012 at 5:09 PM, William G. Scott wgsc...@ucsc.edu wrote: Try this: http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz It seems to behave with nucleic acids correctly, at least in my hands. There is also a newer one (March 10, 2012). Maybe you should try that first. http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.35.tar.gz 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) email: wgsc...@ucsc.edu On Mar 27, 2012, at 1:29 PM, Longfei Wang wrote: Hi there, I've received a bug report about coot. I think this is a good place to report. Here is the summary of the problem. If open a molecule and try to build a new nucleotide, Coot crashes. This happened for the version of Coot 3936, both in Linux and WinCoot. A labmate suspects that there are library issues with regards to PDB version between Coot and REFMAC. An additional issue: Protein residues with hydrogens present can be real space refined in Coot. However, nucleic acid residues with hydrogens present cannot be real space refined in Coot. Attempting to do this results in exploding hydrogens. Best Longfei -- *Longfei Wang * Postdoctoral Fellow Harvard Medical School 250 Longwood Ave Boston, MA 02115 -- *Longfei Wang * Postdoctoral Fellow Harvard Medical School 250 Longwood Ave Boston, MA 02115
Re: [COOT] Coot nucleic acid issue
Try this: http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz It seems to behave with nucleic acids correctly, at least in my hands. There is also a newer one (March 10, 2012). Maybe you should try that first. http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.35.tar.gz 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) email: wgsc...@ucsc.edu On Mar 27, 2012, at 1:29 PM, Longfei Wang wrote: Hi there, I've received a bug report about coot. I think this is a good place to report. Here is the summary of the problem. If open a molecule and try to build a new nucleotide, Coot crashes. This happened for the version of Coot 3936, both in Linux and WinCoot. A labmate suspects that there are library issues with regards to PDB version between Coot and REFMAC. An additional issue: Protein residues with hydrogens present can be real space refined in Coot. However, nucleic acid residues with hydrogens present cannot be real space refined in Coot. Attempting to do this results in exploding hydrogens. Best Longfei -- *Longfei Wang * Postdoctoral Fellow Harvard Medical School 250 Longwood Ave Boston, MA 02115
[COOT] Coot and stereo projector
Howdie: Has anyone had success using coot with a 3D stereo projector? If so, any recommendations? Thanks. Bill William G. Scott Contact info: http://www.chem.ucsc.edu/~wgscott/
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] how to optimize this part in order to have the green blobs disappear by Coot
I would be a bit more concerned with the apparent lack of fit of the model to the map. It looks as if there is unoccupied side chain density, and possibly side chains that don't occupy density. It is hard to tell from a snapshot, but if this is the case, make sure everything is in register first, then re-refine, having reset the temperature factors to something sensible, and then when you converge on something that fits and makes sense, re-assess the map. Lots of green density sitting on your model might indicate problems with scaling the data or with the temperature factor refinement. 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 Jan 25, 2012, at 8:04 PM, Dialing Pretty wrote: Dear All, Will you please take a loot on the coot sscreenshot and give me some suggestions on how to further optimize in order to have the green blobs disappear by Coot? Cheers, Dialing
Re: [COOT] GThread-ERROR **: GThread system may only be initialized once.
On Jan 26, 2012, at 5:36 AM, Bernhard Lohkamp wrote: Hope this resolves the problem, B Seems to fix it on OS X -- Bill
Re: [COOT] Coot 0.6.2 and X11
Well, I just build a version for 10.6, and haven't had a chance to point anyone to its web location, so I am guessing you installed the one I compiled for 10.7…. So please try this one and lemme know if it works please. Bill http://sage.ucsc.edu/~wgscott/coot/ 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) email:wgsc...@ucsc.edu On Dec 9, 2011, at 3:08 PM, Matthew J. Whitley wrote: Hello all, Today I upgraded Coot from version 0.6.1 to 0.6.2 on my Mac (OS X 10.6.8). The installation was successful, but now Coot won't run anymore. When I start the program, I get the following error: dyld: Library not loaded: /usr/X11/lib/libX11.6.dylib Referenced from: /Library/Coot/bin/coot-real Reason: Incompatible library version: coot-real requires version 10.0.0 or later, but libX11.6.dylib provides version 9.0.0 /usr/local/bin/coot: line 7: 62920 Trace/BPT trap /Library/Coot/bin/coot-real $@ Any ideas? Thanks, Matthew Whitley
Re: [COOT] Coot for OSX 10.6
Hi Phil: I haven't been able to compile coot since 11 September, due to a change in the code. I've got a 10.6.8 version of that too, but nothing newer I am afraid. Sorry. Bill On Oct 31, 2011, at 5:11 AM, Phil Evans wrote: As I understand it, Bill Scott now only builds Coot for OSX 10.7: is that right? At least his recent stand-alone builds don't seem to work with 10.6 Is there an up-to-date(ish) Coot build for 10.6? I hesitate to build it myself and I dislike Fink Phil
Re: [COOT] key binding on OS X 10.7
On Oct 24, 2011, at 8:01 AM, Paul Emsley wrote: I have switched from the COOT I compiled from fink to Bill's binary COOT, the situation has not changed. They are both compiled with fink. The only difference is the top-level directory is /LIbrary/Coot instead of /sw
Re: [COOT] Stereo on a Mac
Hi Andrew: I don't have the hardware to test it on, but as far as I am aware, it will do active stereo. At least that is the intention. Bill PS: I'm compiling various versions of 0.6.2. Somehow I missed the fact that the stable release had come out two weeks ago. Sorry. On Jul 7, 2011, at 12:48 PM, Andrew T. Torelli wrote: Hi everyone, The recent post about running coot on a powermac G5 has me a little confused because I thought the only option for stereo on a Mac was to use a Zalman monitor for passive stereo. I'm clearly missing something. Is it true that active stereo with 120 Hz LCD monitors is not possible with a Mac? I'm considering taking the plunge to switch over to Mac entirely, but one source of hesitation is that I prefer active stereo and would like to move to LCDs if possible. Assuming I'm still correct that 120 Hz LCD active stereo is not compatible with Macs, is it also true that this is unlikely to change in the foreseeable future (i.e. Apple or Nvidia don't see enough financial benefit to correct the problems ergo there is little driving force)? Thank you for the enlightenment, -Andy Torelli -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Mark J van Raaij Sent: Sunday, July 03, 2011 5:53 AM To: COOT@JISCMAIL.AC.UK Subject: Re: coot on powermac G5 running Tiger Hi Juergen, I have tried using fink before, but a precompiled binary would be easier... I think Snow Leopard is incompatible with the G5 (and with ppc in general). Leopard would work, I might try this if I can get an installation disk and nobody has a binary compiled for 10.4 (Bill Scotts page does not have it anymore for new versions of coot). There are some rumours that Leopard broke the stereo, but also that the latest updates fix it again. Mark Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campus Cantoblanco E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/content/research/macromolecular/mvraaij On 2 Jul 2011, at 16:25, Bosch, Juergen wrote: Hi Mark, have you ever tried using fink ? You don't need to do much to compile it yourself with the help of fink. Here's the link to fink (or better to Bill Scott's fink it yourself page) http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled You will need Apple's Xcode, which you can get after registration for free. Once you have installed fink you really only type fink install [name of program you want], hit a couple of times y (yes) or whatever default value is requested. You have to do the usual edits in your .bashrc or .cshrc file to point X11 to your fink binary. You also have the option to download precompiled binaries, but not sure if Bill keeps still 10.4 - you might want to upgrade to Snow Leopard. Jürgen On Jul 2, 2011, at 7:28 AM, Mark J van Raaij wrote: Dear All, My second computer in the office is a Powermac G5 with MaxOSX 10.4 equipped with a stereo-capable CRT and Nuvision emitter/glasses. I would like to install coot on this, pref. prebuilt because I am hopeless at compiling... The most recent build I could find is 0.5.2 ueno on Bill Scotts website - anyone know of a more recent version compiled and compatible with our system. would stereo work with a more recent version of coot? greetings, Mark .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [COOT] Python problem
Dear Phil, Paul, Ben, Bernhard et al: Sorry to arrive 8 hours late to the party, but first my apologies to Phil. I thought I had fixed this problem by excising from the coot wrapper script the path in /System/Library, i.e., export PYTHONPATH=/Library/Coot/lib/python2.7/site-packages:/Library/Coot/lib/python2.7/site-packages/gtk-2.0:/Library/Coot/share/coot/python:$PYTHONPATH So my guess is you have $PYTHONPATH or else my fix somehow doesn't work. The reason this is problematic is ultimately because coot is using python 2.7 libraries (included). (Old whine, new bottle.) Anyway, it would be good to find which is the source of the problem. I think I need to add to PYTHONPATH to keep phenix happy, but if the user has set $PYTHONPATH, then what is in the wrapper script becomes fragile. Any feedback will help me make this better. Thanks. Bill On May 4, 2011, at 5:33 AM, Phil Evans wrote: OK that worked thanks I'm not sure whether these files got copied over from my old machine - I didn't do the copy myslef Phil On 4 May 2011, at 13:16, Paul Emsley wrote: On 04/05/11 13:11, Phil Evans wrote: Is that dangerous? Not really, python makes the pyc files again (I understand). If I move it I then get ImportError: Bad magic number in /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyc after moving that I then get ImportError: Bad magic number in /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/os.pyc and so on I guess So I understand after a bit more googling. I should have recommended some sort of find: $ find /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6 -name *.pyc -delete
Re: [COOT] Python problem
I'm hosting nightly builds now, and none of the more recent versions should have this in the wrapper script. Please let me know if somehow that isn't the case. Bill On May 4, 2011, at 9:10 AM, Phil Evans wrote: I did delete the *.pyc files in the system directories, and they have now reappeared I've also edited the coot wrapper to remove the system directories as suggested by Bill. All seems to work now thanks to everybody Phil On 4 May 2011, at 15:29, Ben Eisenbraun wrote: On Wed, May 04, 2011 at 01:16:29PM +0100, Paul Emsley wrote: On 04/05/11 13:11, Phil Evans wrote: Is that dangerous? Not really, python makes the pyc files again (I understand). Yes, but you're deleting compiled python objects from _system_ directories, and since normal users can't write to those directories, they will be recompiled and then thrown away every time python is run and those modules are imported. If I move it I then get ImportError: Bad magic number in /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyc after moving that I then get ImportError: Bad magic number in /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/os.pyc and so on I guess The problem is probably the PYTHONPATH setting in the coot wrapper script. If you're using a recent Fink/Bill Scott build of Coot, then it is using Python 2.7, and putting the 2.5 and 2.6 directories in the PYTHONPATH causes the interpreter to barf on start up. There was a discussion about this on the CCP4bb a couple months ago: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A1=ind1103L=CCP4BB#25 -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Re: [COOT] New Coot plugin for RNA building
Nice. Seems to work fine in the OS X version as well... in my 60 seconds of testing. Bill On Mar 31, 2011, at 12:58 PM, Kevin Keating wrote: I've just released a new Coot plugin to help with building RNA structure, so I wanted to make a quick announcement to the mailing list for any interested RNA crystallographers. The plugin, named RCrane, is free for use and can be downloaded from http://www.pylelab.org/software/index.html#rcrane. There are also several screenshots on that site for anybody who's curious. RCrane helps with placing phosphates and bases into electron density, and then automatically determines coordinates for the remainder of the backbone. It's designed for use in maps of up to ~4 A resolution, and requires a very recent nightly build of Coot (downloadable from http://lmb.bioch.ox.ac.uk/coot/devel/build-info.html). The plugin has been tested under Windows and Linux. It should work under OS X if you have a recent enough build of Coot, although I haven't done any testing there yet. For anybody who tries out the plugin: feel free to send me any bug reports or suggestions and I'll try to incorporate them into future versions. Thanks, Kevin
[COOT] Stand-Alone Coot -automated builds for OS X 10.6.X 64-bit
I'm attempting to generate automated builds of coot pre-releases for OS X 10.6.X users. These are 64-bit. If all works well, there should be a new one every day (assuming a new source tarball is available). http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot Please let me know if it is problematic. Thanks. -- Bill Scott
[COOT] coot on OS X 10.4
Has anyone managed to compile a recent version of coot on OS X 10.4.X via fink? Thanks. Bill Scott
Re: [COOT] Installation problems: Coot for OS X - from CCP4 / Fink
Dear Antony: First, allow me to apologize for this. I was hoping this would help make everything seamless. Mark Brooks suggested updating X11 from http://xquartz.macosforge.org/trac/wiki . Although this might help with such a problem on 10.5 with ppc., in this case I believe it shouldn't help, because on 10.6, this X11 doesn't get installed in the usual location, but instead somewhere in /opt I think. In any case, I don't use it on 10.6, so coot won't have been compiled using it, so installing it should neither help nor hurt. Coot simply won't see it. If coot does see it, it suggests you have the environment variable $DYLID_LIBRARY_PATH set. (Doing so is a very bad idea.) The short answer is I really don't know what is causing this problem. I have two suggestions: (1) Try building coot on your machine and see if it produces a working version. It could be the old iMac I build these things on has some problem with its configuration or something. (2) Try installing my new pre-compiled stand-alone version from here: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot#Version_0.6.2-pre-1-3250 Please let me know what happens. After term ends (this week) I will have more time to devote to this. Bill PS: Also, if you or anyone has run into a problem with coot on OS X, please put my email address in the To line and then I'll be sure to see it right away... On Dec 1, 2010, at 2:41 AM, Antony Oliver 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
[COOT] Stand-Alone Coot - 0.6.2 pre-release svn rev. 3072 OS X 10.6 64-bit, phenix-compliant
Sorry I haven't done this until now. Been distracted by the struggle for survival. http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot#Version_0.6.2-pre-1-3072
Re: [COOT] PyGTK in standalone OS X builds
Check /usr/local/xtal/coot64/bin/coot to see if I set $PYTHONPATH right. It should have /usr/local/xtal/coot64/lib/python2.6/site-packages/gtk-2.0 Nathaniel Echols wrote: When I use the 0.6.1 package from Bill's web site, I get this error when I try to start the Python scripting GUI: COOT_PYTHON_DIR was defined to be /usr/local/xtal/coot64/share/coot/python but no PyGtk and hence no coot_gui. Not sure what to do about this, because it appears to have the module installed: nat:~ ls /usr/local/xtal/coot64/lib/python2.6/site-packages/ README cairo gtk-2.0 numpy numpy-1.3.0-py2.6.egg-info pygtk.pth pygtk.py pygtk.pyo thanks, Nat
Re: [COOT] Problem reloading Coot.
Did you issue source /sw64/bin/init.sh (or init.csh if you are a tcsh user) first? This sets $PATH and some other needed environment variables. On May 4, 2010, at 6:01 AM, David Lisgarten wrote: Dear Coot, I recently installed Coot version (0.6.1 64 intel) on a iMac 10.6. using Fink , 64 bit (Fink installed via bootstrap). I used the command sudo apt-get install coot and everthing seemed fine. On entering command coot, software loaded successfuly. However after I logged out and then logged in I couldn't re-load Coot. Thanks, David.
Re: [COOT] Ligands
If you can define a SMILES string for your ligand, you can get coot to build the ligand with the press of a button in a fraction of a second. If the SMILES syntax is a PITA, use this: http://www.molinspiration.com/cgi-bin/properties If you need more options, phenix.elbow also permits you to use a SMILES string input. Dean Derbyshire wrote: Perhaps (most likely in fact) this has been asked and addressed in the past: is there (or will there be) a way in COOT to 'build' ligands from scratch? Currently I go through a long winded route of Sketcher... importing and pulling the coords around to fit electron density... then finally idealising the geometry. What do other people do? Thanks in advance Dean
Re: [COOT] [ccp4bb] coot and probe clash
On Feb 8, 2010, at 2:07 PM, Nathaniel Echols wrote: On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott wgsc...@chemistry.ucsc.edu wrote: This is available to install as a binary from here: http://molprobity.biochem.duke.edu/get_molprobity.php Although probe and MolProbity3 are said to be free and open source software distributed under a BSD-style license, I can't find the source code, so I can't make coot depend on it within fink. http://kinemage.biochem.duke.edu/software/probe.php and Reduce (also required for Coot, I think) is here: http://kinemage.biochem.duke.edu/software/reduce.php -Nat OK, I have added both now to fink cvs (unstable branch). Feedback appreciated.
Re: [COOT] Coot 0.52 on OSX not showing molecule
Any ideas? -Sam Try something more recent.
Re: [COOT] Coot dependency problem? Power PC G4
Dear Richard: It looks like I neglected to add this as a dependency. Please try installing libcurl4-shlibs, and hopefully that will solve the problem. If not, please let me know as soon as possible. Bill On Jan 17, 2010, at 12:33 PM, Richard Kingston wrote: Hello Bill After updating to the latest version of your coot binary distribution (coot-0.6.1-pre-1-1), I'm getting the following error on a Power PC G4, when I try and run it. dyld: Library not loaded: /sw/lib/libcurl.4.dylib Referenced from: /sw/bin/coot-real Reason: Incompatible library version: coot-real requires version 6.0.0 or later, but libcurl.4.dylib provides version 5.0.0 /sw/bin/coot: line 5: 342 Trace/BPT trap /sw/bin/coot-real $@ The previous iteration ( coot-0.6.0-1) was working fine (after rebuilding and reinstalling gmp, as per usual). Anyway, maybe you have time to look into it. Or maybe there's something peculiar about my local configuration. Regardless, I really appreciate the time you've spent maintaining and distributing scientific software to the Mac community. This has been enormously helpful to may of us. Best, Richard Richard Kingston, PhD. School of Biological Sciences The University of Auckland New Zealand website: http://persephone.sbs.auckland.ac.nz/richard/lab/
Re: [COOT] SGI dials and coot?
On Jan 11, 2010, at 4:38 AM, Andreas Förster wrote: Every time I'd ask a question You really ought to update. 0.1 is a bit long in the beak.
[COOT] OS X /fink coot update problems
Yo: Several people wrote to me in the last couple of days about different problems with respect to the latest coot update in fink. This all happened at the beginning of term so I haven't really had enough time to deal with this systematically. Briefly, I put coot 0.6 is in the stable and unstable branch of fink sometime around the Unorthodox Holiday. Subsequently I updated two dependency packages in the unstable branch of fink: guile18-gtk and clipper, and then updated to one of the 0.6.1 pre-releases in unstable (revision-2678). I don't want to touch what is in stable until I know it is in fact stable. Any or all of these could have created problems (although I tested these on a variety of machines and didn't notice anything). If you run the command % fink list -i coot clipper guile18-gtk you should see something like this: Information about 8154 packages read in 1 seconds. i clipper-shlibs 1:2.1-14 Object-oriented crystallographic libraries i coot 0.6.1-pre-1-1 Crystallographic molecular graphics i coot-shlibs 0.6.1-pre-1-1 Crystallographic molecular graphics i guile18-gtk 2.1-2 Glue code to link gtk to guile i guile18-gtk-shlibs 2.1-2 Glue code to link gtk to guile If you have earlier versions, please update. I also recommend (a) having the most recent version of Xcode (the apple compilers, etc) compatible with your OS (b) Apple's official X11 distribution if you are on 10.6 or plan to update to 10.6. (c) if you have a 64-bit capable machine, use the 64-bit fink, ccp4, etc. as this is the future If I haven't gotten back to you, email me again please, and include every relevant detail (version of OS X, fink version, Xcode version, X11 version, output of above command, etc.) and I will do my best to try to deduce what might be problematic. Meanwhile, please accept my apologies. Bill
Re: [COOT] coot 0.6.1-pre update - osx 10.6 - problem with mtz and map files
Are you using the 32-bit or 64-bit coot? I have to confess only having checked the 64-bit version (which worked ok in my hands). On Jan 7, 2010, at 9:31 PM, Jan Abendroth wrote: Hi all, I am trying to update coot on osx 10.6 from a 0.6-pre version to the current fink version (0.6.1-pre). Doing the usual fink spiel (fink selfupdate, fink index ...) I ran into some issues during 'fink update-all': a few packages that are dbus and dbus-dependent would not install. All the rest of the core packages could be installed manually. Coot now would install just fine (fink install coot) after I removed the old installation (fink remove coot). Now coot starts up fine as 0.6.1, coordinates can be read, analyzed and modified. However, I cannot read in maps from mtz files, see message from the xterminal below. Coot actually totally freezes in this process. Similarly, ccp4 maps cannot be read in either due to a issue with space groups. Any ideas would be highly welcome Jan reading in mtz file ... initalize graphics molecules...done. (handle-read-draw-molecule-with-recentre 204964c6_2009-10-26_als503_i213_xds_refmac21-coot-Ab31.pdb 1) Reading coordinate file: 204964c6_2009-10-26_als503_i213_xds_refmac21-coot-Ab31.pdb PDB file 204964c6_2009-10-26_als503_i213_xds_refmac21-coot-Ab31.pdb has been read. Spacegroup: I 21 3 Cell: 135.38 135.38 135.38 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 170/172 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: NCS found from matching Chain B onto Chain A Molecule 0 read successfully coot-real(86853,0xa01cd500) malloc: *** error for object 0x2650a00: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug [... same message many times over ...] Spacegroup_registry: ASU warning, LGhash=0x Spacegroup_registry: ASU fail INFO:: not an mtz file: 204964c6_2009-10-26_als503_i213_xds_refmac21.mtz reading in a ccp4 style map: saved directory name: /Users/jan/deCODE/ssgcid/AnphA.01382.a/ccp4/ CCP4 map filename: /Users/jan/deCODE/ssgcid/AnphA.01382.a/ccp4/204964c6_2009-10-26_als503_i213_xds_refmac21_2Fofc.map INFO:: map file type was determined to be CCP4 type allocating space in read_ccp4_map attempting to read CCP4 map: /Users/jan/deCODE/ssgcid/AnphA.01382.a/ccp4/204964c6_2009-10-26_als503_i213_xds_refmac21_2Fofc.map Spgr_cacheobj: symops fail -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
Re: [COOT] Scripting missing in CCP4 distribution of COOT v0.6.0 CCP4 (OS X 10.4+ universal dmg installer)
No problem. The hope is that with fink, anyone can compile and install coot without drama on OS X ppc or intel, 10.6, 10.5, 10.4 (there is no 10.6 ppc). On Jan 5, 2010, at 6:13 AM, Huw Jenkins wrote: On 5 Jan 2010, at 13:57, William G. Scott wrote: If you use what is in fink, it will build coot for whatever version of os x you currently have. Apologies I was being stupid, I hadn't realised there were still fink packages for 10.5/10.4 and it was just the binaries that are 10.6 only. I'll give that a go. Cheers, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology Room 8.53 Garstang Building University of Leeds Leeds, LS2 9JT +44(0)113 343 4269 h.t.jenk...@leeds.ac.uk
Re: [COOT] Scripting missing in CCP4 distribution of COOT v0.6.0 CCP4 (OS X 10.4+ universal dmg installer)
See if this works: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot#Stable_Release_for_Intel:__coot-0.6_for_64-bit_Intel_10.6 On Jan 4, 2010, at 2:58 PM, Huw Jenkins wrote: On 4 Jan 2010, at 22:21, Nathaniel Echols wrote: The package distributed by CCP4 was not compiled with support for either Scheme or Python. I'm pretty sure this isn't something you can patch, so you'll need to use one of Bill's tarballs or the Fink distribution. Cheers for the info. I was confused as to why all the Scheme scripts were present in /Applications/coot.app/Contents/coot/share/coot/scheme/ but not being read on start-up. Thanks again, Huw -- Dr Huw Jenkins Astbury Centre University of Leeds
Re: [COOT] 120hz LCDs and coot stereo
Just get a $300 Zalman LCD monitor and use coot with that. No special hardware required and it is OS independent. I'm using it also as my primary monitor as I type this. Michael J Miley wrote: I have a linux workstation with a nvidia quadro graphics card and matching emitter/lcd glasses setup from realD. It is very hard to find CRTs that are able to support the high refresh rates needed for headache free 3D viewing. The old SGI one I have is terrible, as it flickers bad in 3d mode. My question is can i use one of these new 120hz LCD monitors with the above setup for coot. Basically just switch out the crt for the LCD. Has anyone tried this? I am aware that these monitors with a non-quadro nvidia card plus the nvidia emitter/glasses setup will not work with coot. But i think the reason is that the drivers for these non-quadro cards do not support true quad buffered stereo. -- Michael J Miley, PhD Research Assistant Professor Director, Biomolecular X-Ray Crystallography Facility University of North Carolina at Chapel Hill Dept of Pharmacology, CB# 7365 Medical School Building B, Room 124 mjmi...@email.unc.edu Office: 919-843-7174 Cell: 919-451-3593
Re: [COOT] fink coot : unstable branch
On Nov 2, 2009, at 3:59 PM, Bryan W. Lepore wrote: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Installing_Coot_on_OS_X Be sure to use the so-called unstable branch of fink to get the latest pre-releases of coot do i read this correctly : it means ONLY pre-releases, right? and then : `fink -y install coot` [...] whenever you require the latest version. means precisely that - the latest version, NOT a pre-release, so that the unstable branch does not need activation. -bryan This is why I gave up my first career as an international peace mediator in the Middle East. I don't think I consciously distinguished between pre-release and release when I wrote this. In any case, the latest coot will always be in unstable. For a long time, the version of coot in stable was 0.5.2, but I had to make so many changes to get coot to compile as 64-bit on 10.6 64-bit fink but compile as 32-bit on 32-bit fink on 10.6, I didn't want to go back to 0.5.2, so I put the same pre-release into stable as a placeholder that (hopefully) compiles on every permutation of fink and Apple hardware and operating system. When version 0.6 comes out, I will keep that in stable and then again put pre-releases in unstable.
Re: [COOT] Coot 2396 troubles
This happened on a new snow leopard install. It looks like that Apple decided not to include any .la with their X11 SDK. Yes, unfortunately the only way to deal with this is to delete all the *.la files in /sw that make reference to the nonexistent libs or other *.la files. I found the easiest way is to use the z-shell's recursive globbing property: % sudo /bin/zsh # cd /sw/lib # rm -f **/*.la # exit On Oct 6, 2009, at 10:10 AM, Dima Chirgadze wrote: Dear Bill, I am sorry to trouble you again. The new version of coot (2396) failed to install. -- snip --grep: /usr/X11/lib/libXext.la: No such file or directory sed: /usr/X11/lib/libXext.la: No such file or directory libtool: link: `/usr/X11/lib/libXext.la' is not a valid libtool archive make[1]: *** [libcoot-surface.la] Error 1 make: *** [all-recursive] Error 1 ### execution of /var/tmp/tmp.1.XhdXJD failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-coot-0.6-pre-1-revision-2396-1 (Reading database ... 70299 files and directories currently installed.) Removing fink-buildlock-coot-0.6-pre-1-revision-2396-1 ... Failed: phase compiling: coot-0.6-pre-1-revision-2396-1 failed -- snip -- This happened on a new snow leopard install. It looks like that Apple decided not to include any .la with their X11 SDK. Is there anyway to fix this? Thanks again, Regards, Dima
[COOT] I wish I could lose weight like this (OS X 10.6)
Hi Folks: On OS X, 10.6, I have been playing around with hfsCompression. I can decrease the size of /sw/share/coot significantly: % cd /sw/share/ % du -h -d 0 coot 180Mcoot % sudo mv coot coot.1 % sudo ditto --hfsCompress coot.1 coot % du -h -d 0 coot 31Mcoot This can also be done with the libraries and binaries, and even the whole of /sw. It squeezed phenix down to 319 MB from 1.1 GB. CCP4's new footprint is 562 MB, instead of 1.5 GB. hfscompressing Xray data results in a factor of two space-saving. The files still look the same from the point of view of the operating system. You can in fact only see the compression using commands like du or df. More here: http://www.macosxhints.com/article.php?story=20090902223042255 Bill
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.
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
Paul just pulled off a heroic fix (rev 2310). Please try that. On Sep 11, 2009, at 7:40 AM, William G. Scott wrote: Dear Christian: I'm getting it now too. I forgot to cc you. I get it on 32-bit but not 64-bit SL. I've sent the crash report to Paul . Check to see if you have anything in ~/Library/Logs/DiagnosticReports that has coot in the title and a recent date. Bill 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, Christian Am 08.09.09 16:14 schrieb William G. Scott unter wgsc...@chemistry.ucsc.edu : Hi Christian: I just committed coot 0.6-pre-1-revision-2283 to fink cvs. It fixes a bug on 64-bit where the menu would freeze when superposition is invoked. I suppose there is a 0.001 chance that it fixes the other problem too. I have no way to test on 10.5 intel (I still have 10.6) and haven't had direct access to 10.4 for a long time. This could be a problem with coot or with one of many of its ca. 230 dependencies. From what I have read, you can upgrade directly to SL (US $30, UK £25), despite the propaganda on the box. I have ccp4 and coot and the other crystallographic fink things running all in 64-bit now. I'm hoping these will now pass the 70S ribosome test. I hope this works in the meantime. Bill On Sep 8, 2009, at 5:08 AM, Christian Benda wrote: Dear all, we have updated coot to 0.6-pre-1 revision 2264 using fink on our Macs running 10.4.11 to be able to use zalman stereo. Unfortunately it seems like this coot or the combination is not working correctly. So far, there are two main issues: 1. coot freezes and closes down after selecting e.g. the preferences menue 2. coot writes an empty 0-coot.state.scm file no matter what's loaded into coot. Any hints to what we can do? We really need the stereo and therefore revision 2225 or higher Many thanks in advance Christian Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: be...@biochem.mpg.de
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
On Sep 11, 2009, at 7:36 AM, Benda, Christian wrote: hink it's time to upgrade to 10.6, finally! 10.6.1 now. :D
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
I'm going to make a wild guess and suggest it is a python version mismatch. If you open the python scripting window and type in help() what do you see in the console window? I get this: BL INFO:: command input is: help() Welcome to Python 2.6! This is the online help utility. On Sep 8, 2009, at 10:47 AM, Engin Ozkan wrote: Hi everybody, Using the revision 2283 on 10.5, I am seeing this whenever I am closing the application: /sw/bin/coot: line 5: 19785 Segmentation fault /sw/bin/coot- real $@ Yep, coot shuts down with a segmentation fault. I haven't tested most functionality and it has not affected my use of coot yet, but I assumed it might help to report it. This seems to be the same bug observed by Christian on a 10.4 machine, because I get the similar Preferences crash. Empty 0-coot.state.scm is also probably due to the crash during exiting. Engin On 9/8/09 7:14 AM, William G. Scott wrote: Hi Christian: I just committed coot 0.6-pre-1-revision-2283 to fink cvs. It fixes a bug on 64-bit where the menu would freeze when superposition is invoked. I suppose there is a 0.001 chance that it fixes the other problem too. I have no way to test on 10.5 intel (I still have 10.6) and haven't had direct access to 10.4 for a long time. This could be a problem with coot or with one of many of its ca. 230 dependencies. From what I have read, you can upgrade directly to SL (US $30, UK £25), despite the propaganda on the box. I have ccp4 and coot and the other crystallographic fink things running all in 64-bit now. I'm hoping these will now pass the 70S ribosome test. I hope this works in the meantime. Bill On Sep 8, 2009, at 5:08 AM, Christian Benda wrote: Dear all, we have updated coot to 0.6-pre-1 revision 2264 using fink on our Macs running 10.4.11 to be able to use zalman stereo. Unfortunately it seems like this coot or the combination is not working correctly. So far, there are two main issues: 1. coot freezes and closes down after selecting e.g. the preferences menue 2. coot writes an empty 0-coot.state.scm file no matter what's loaded into coot. Any hints to what we can do? We really need the stereo and therefore revision 2225 or higher Many thanks in advance Christian Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: be...@biochem.mpg.de -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11
Hi Christian: I just committed coot 0.6-pre-1-revision-2283 to fink cvs. It fixes a bug on 64-bit where the menu would freeze when superposition is invoked. I suppose there is a 0.001 chance that it fixes the other problem too. I have no way to test on 10.5 intel (I still have 10.6) and haven't had direct access to 10.4 for a long time. This could be a problem with coot or with one of many of its ca. 230 dependencies. From what I have read, you can upgrade directly to SL (US $30, UK £25), despite the propaganda on the box. I have ccp4 and coot and the other crystallographic fink things running all in 64-bit now. I'm hoping these will now pass the 70S ribosome test. I hope this works in the meantime. Bill On Sep 8, 2009, at 5:08 AM, Christian Benda wrote: Dear all, we have updated coot to 0.6-pre-1 revision 2264 using fink on our Macs running 10.4.11 to be able to use zalman stereo. Unfortunately it seems like this coot or the combination is not working correctly. So far, there are two main issues: 1. coot freezes and closes down after selecting e.g. the preferences menue 2. coot writes an empty 0-coot.state.scm file no matter what's loaded into coot. Any hints to what we can do? We really need the stereo and therefore revision 2225 or higher Many thanks in advance Christian Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: be...@biochem.mpg.de
Re: [COOT] Coot osx 10.6 problem
The good news is I can reproduce your error: checking for GtkGLExt - version = 1.0.0... no *** Could not run GtkGLExt test program, checking why... *** The test program failed to compile or link. See the file config.log for the *** exact error that occured. This usually means GtkGLExt is incorrectly installed. ### execution of /var/tmp/tmp.2.JleDIx failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-coot-0.6-pre-1-revision-2283-1 (Reading database ... 201033 files and directories currently installed.) I'm coming to the conclusion that upgrading 32-bit fink to SL on a 64- bit capable machine is more trouble than a fresh install of 64-bit fink. I'll try to get this sorted out. Sorry. Bill On Sep 8, 2009, at 7:30 AM, Dima Chirgadze wrote: Dear Bill, I am having problems installing latest version of coot under snow leopard. 1) I have installed fink 0.29.9 (32-bit) via bootstrapping on a Snow Leopard machine. 2) changed the /sw/etc/fink.conf according to your website and updated fink 3) changed /sw/etc/apt/sources.list to include deb http://sage.ucsc.edu/fink_intel_10.6_32bit stable main crypto deb http://sage.ucsc.edu/fink_intel_10.6_32bit unstable main crypto deb http://sage.ucsc.edu/fink_intel_10.6_32bit local main 4) when I do: fink -b install coot, it installs/updates about 100 packages and then I get the following error: --snip-- checking for pkg-config... (cached) /sw/bin/pkg-config checking for GtkGLExt - version = 1.0.0... no *** Could not run GtkGLExt test program, checking why... *** The test program failed to compile or link. See the file config.log for the *** exact error that occured. This usually means GtkGLExt is incorrectly installed. ### execution of /var/tmp/tmp.2.MhYZKK failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-coot-0.6-pre-1-revision-2265-1 (Reading database ... 25946 files and directories currently installed.) Removing fink-buildlock-coot-0.6-pre-1-revision-2265-1 ... Failed: phase compiling: coot-0.6-pre-1-revision-2265-1 failed --snip-- I've searched the lists but couldn't get it working I tried re-installing gtkglext1 and gtkglext1-shlibs. The $LD_LIBRARY_PATH and/or $DYLD_LIBRARY_PATH both are unset. I still cannot install. Could you please help me to resolve it? Thank you very much in advance, Regards, Dima Dimitri (aka Dima) Chirgadze, PhD Senior Research Associate Department of Biochemistry University of Cambridge Cambridge, CB2 1GA UK Tel: +44 1223 766029 Fax: +44 1223 766082
[COOT] Need help with coot wiki
I just started a stereographics section on the coot wiki, but need help, specifically with the hardware stereo part from someone with firsthand experience, but feel free to improve all of it: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Stereographic_Display
Re: [COOT] MacOS and Zalman
On Aug 19, 2009, at 1:14 AM, Lutz Schmitt wrote: Dear Bill, I am probably one of the many people out here who asked you a question concerning the Zalman 3D monitor. We got one yesterday and I upgraded coot to coot 0.6-pre-1 (revision 2215) running on a Quad-Core Intel with a NVidia Qudro FX 5600 (=S 10.5.7). I use the DVI cable, mirroring off and the Zalman is the second monitor. Running coot at the highest resolution 1680x1050 and 60 Hz (more is not possible according to the monitor settings) I have the feeling that I close but not really there. In coot, I can see two images, the 3D effect is there but not perfect yet and without the polarize glasses the screen flickers. However, the situation reminds me of using Crystal eyes and a refresh rate, which is too small meaning I am almost there. I think you can increase the stereo angle. I need to appeal to Paul or Bernhard for the appropriate command (hence the cc to the cootbb). Does it work ok with pymol? Do you know what I am doing wrong? No. Quite possibly nothing. It is also possible you are seeing the exact same thing as I am, but because of my small brain and limited cranial capacity, I get a different visual effect. BTW, I still use bash not zsh. Therefore I have not used your scripts yet. You can run any shell script (including zsh functions) by making it executable and run it in the usual way from one of the other shells. Many thanks in advance Lutz
Re: [COOT] MacOS and Zalman
On Aug 19, 2009, at 8:21 AM, Paul Fyfe wrote: (set-hardware-stereo-angle-factor 1.3) This is I think the command I was after. Thanks.
Re: [COOT] MacOS and Zalman
Hi Lutz:
On Aug 19, 2009, at 11:59 AM, Lutz Schmitt wrote:
Hi Bill,
thanks! But now comes the ignorant part from my site :-)
As a non-native speaker, I do understand AFAIK (as far as I know?),
but what do you mean by fwiw? - sorry
Hence the wtf utility:
% fink list wtf
Information about 9261 packages read in 3 seconds.
i wtf 20080626-1 Translates common
Internet acronyms
% wtf fwiw
FWIW: for what it's worth
% wtf afaik
AFAIK: as far as I know
% wtf wtf
WTF: {what,when,where,who,why} the f---
Furthermore, I use coot and Macs and I appreciated more than once
all your input. Since you did such a wonderful job, I have never
bothered much with fiddling around with coot. I just took what you
developed. Therefore, I have to ask the stupid and ignorant
question: how do I issue a scheme??
You can issue commands in either the scheme scripting language or the
python scripting language.
To issue a scheme command, just do the following:
1. Start coot and go to the Calculate menu item.
2. In the pull-down, the second-to-last entry is Scripting Go
to that and select the Scheme option.
3. Paste in the command (zalman-stereo-mode) including the
parentheses into the top window where it says Command:
4. Hit the return key and you should now be getting a double image.
In other words, could you please direct me to your scheme or send it
to me? I hope that the fact that I still stick to bash and have not
changed to zsh makes no problem. Again, blame my ignorance!
Don't worry, it has nothing to do with what shell you choose. It will
work the same whether you use bash/zsh/tcsh.
Sorry for my ignorance
Never apologize for asking questions. If you do a mail search, you
will see that I am the ignorance king.
But if you are feeling adventurous, right-click on the second line of
the menu bar in the blank area next to where it says Display
Manager. Select Add a user-defined button and make yourself a
Zalman Stereo button, and then feel smug about what a power user you
now are.
I think you will need the python version of the command, instead of
the scheme version, which is zalman_stereo_mode()
Note the underscores and different placement of the parentheses.
There is even an appropriate icon in row five, column eight, you can
select when prompted for an icon.
Lutz
Am 19.08.2009 um 20:41 schrieb William G. Scott:
Hi Lutz:
Yeah, that is definitely the problem. That kind of hardware
stereo is for a CRT and the special video card it needs.
Fortunately, we don't need any of that.
Try issuing the scheme command
(zalman-stereo-mode)
AFAIK, it is not yet implemented as a menu item (but you can make
one, which is what I did).
I am also using the DVI cable and adaptor, fwiw.
Bill
William G. Scott
contact info: http://chemistry.ucsc.edu/~wgscott
On Aug 19, 2009, at 11:36 AM, Lutz Schmitt wrote:
Hi Bill,
yes I have a first-generation airbook as well. I started coot,
moved the coot window to the Zalman monitor and used draw,
stereo, hardware stereo to activate it, but as I said coot
told me that stereo was not possible. Should I start to force
coot to start on the Zalman? If so, do I have to make the Zalman
the primary screen?
Cheers
Lutz
Am 19.08.2009 um 19:01 schrieb William Scott:
Hi Lutz:
Yes, mine is working with a first-generation airbook. I didn't
do anything special. How are you activating stereo on coot (what
command)?
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Aug 19, 2009, at 9:59 AM, Lutz Schmitt wrote:
Dear Bill,
many thanks!
Well with pymol the same - near there but only nearly.
I did two more thing so far. Installed the newest coot release
on my airbook and simply connected the Zalman (VGA connector).
Here, coot tells me that stereo can not be enabled and
nothing happend. According to your email to Jürgen, you got it
to work on your Airbook. Or am I missing something?
Furthermore, I checked the quadro compatibility list of Zalman -
it ends with the FX 5500, the 5600 is not included. Is that a
possible explanation. We have another Mac with the FX 4500
installed. According to the list it should be supported (at
least on XP).
But most of all - I am really interested to learn about the
stereo angle :-)
Cheers
Lutz
Am 19.08.2009 um 16:36 schrieb William G. Scott:
On Aug 19, 2009, at 1:14 AM, Lutz Schmitt wrote:
Dear Bill,
I am probably one of the many people out here who asked you a
question concerning the Zalman 3D monitor.
We got one yesterday and I upgraded coot to coot 0.6-pre-1
(revision 2215) running on a Quad-Core Intel with a NVidia
Qudro FX 5600 (=S 10.5.7). I use the DVI cable, mirroring off
and the Zalman is the second monitor.
Running coot at the highest resolution 1680x1050 and 60 Hz
(more is not possible according
Re: [COOT] Zalman Coot
Dear Jürgen: I've been using the DVI cable provided and full resolution (I had to set this manually in display preferences). I assume what works with my mini and my airbook would also work with a macbook pro. I haven't tried the VGA option, but assume that would work too. One thing I discovered is it doesn't work if you have display mirroring on. If that is the case, turn it off in display preferences, and hopefully it will then work. If not, try tilting the screen up or down a little bit (or move your head relative to the screen). I went through a bit of frustration but it was all due to user error on my part. Is the DVI cable just dead? Did you issue the command in coot to start the stereo specific to Zalman mode? Try the latest PyMOL too. You have to rename it MacPyMOLZalman.app first. Then open it, and if it isn't already in stereo, just hit the stereo menu item. Depending on the positioning of the window, and number of pixels, you can have the image reversed, so check to see if that is happening, as it ruins the 3D effect. Good luck. Hope it is working for you soon. Bill On Aug 5, 2009, at 11:46 AM, Jürgen Bosch wrote: Hi Bill, I have received my two Zalmans yesterday and I wanted to try them out today. I don't seem to have the right settings I assume as I get a double vision image e.g. a loop that is supposed to be in the back in 3d splits up and you can see two lines (that's as Calpha). I have played with the resolution of the monitor to decrease it to 768x1024 but the two lines still persist. I'm using the latest 15 MacBookPro via MiniDisplayport to VGA as the DVI does not seem to work with the cable provided by Zalman I assume. My coot is 0.6-pre-1 rev 2037 I turned of spaces and enabled mirroring to keep it simple but I'm not quite happy right now. I have not yet tried Pymol as my version does not support the Zalman monitors. Any suggestions what I can try to get rid of the double lines ? Thanks, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.me.com/bosch_lab/
[COOT] Stereo Coot
Dear Bernhard: Thanks very much for implementing Zalman stereo into coot. I apologize for neglecting to say so in my earlier email, and after previous cootbb emails, I have no excuse (except maybe fatigue). Thanks also for pythonizing coot, by the way, too. All the best, Bill
Re: [COOT] Coot with stereo LCD on OS X
On Jul 29, 2009, at 3:34 AM, Paul Emsley wrote: For me, the reference stereo image is Frodo on a ES PS390. I'm old(e) enough to remember having used that. You might like to tweak the eye angle: set_hardware_stereo_angle_factor(1.45) # or some such (I am presuming that you are using the pythonic version). The mac (fink) versions that we packaged use both python and scheme simultaneously at the same time all at once concurrently and in unison. Thanks to Paul (and Warren) for implementing this. For stereo support of Zalman M220W in Coot, credit should entirely go to Bernhard Lohkamp. Sorry, I fscked up. I have no excuse, given previous email exchanges, except to plead sleep deprivation and juvenile onset senility (but I remember the PS300). Regards, Paul. Tootle pip. Bill
Re: [COOT] problem with install on new Macbook Pro (OS X 10.5)
Hi Jason: For some reason that I don't understand, some users find they need to issue the command source /usr/local/xtal/coot/bin/init.sh prior to issuing the command coot (coot in this context actually invokes a wrapper shell script that has that first source command in it, so that is why I don't understand why it isn't working. If someone who is experiencing this problem feels like trying an experiment, just edit that shell script file /usr/ local/xtal/coot/bin/coot and after the source line, add a line like sleep 5 before the line that invokes coot-real. I can't reproduce the problem, so I can't test this.) Sorry for the inconvenience. Bill On Jun 5, 2009, at 7:56 AM, Jason Greenwald wrote: 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
Re: [COOT] subversion build on ubuntu 9.04 fails : [: =: unary operator expected error
I have the following guile-like stuff installed, if it is of any help:
diablo-% which dpkg-list
dpkg-list () {
dpkg --list \...@\*
}
diablo-% dpkg-list guile | grep ii
ii guile-1.6-libs
1.6.8-6.3ubuntu1 Main Guile libraries
ii guile-1.8
1.8.5+1-4.1ubuntu1 The GNU extension language
and Scheme interp
ii guile-1.8-dev
1.8.5+1-4.1ubuntu1 Development files for Guile 1.8
ii guile-1.8-doc
1.8.5+1-4.1ubuntu1 Documentation for Guile 1.8
ii guile-1.8-libs
1.8.5+1-4.1ubuntu1 Main Guile libraries
ii guile-g-wrap
1.9.11-1.1build1 scripting interface generator
for C - Guile
ii guile-gnome0-canvas
2.15.95-2ubuntu1 Guile bindings for
libgnomecanvas
ii guile-gnome0-glib
2.15.95-2ubuntu1 Guile bindings for GLib
ii guile-goosh
1.3-1Installs goosh
ii guile-gui
0.2-2Installs guile-gui for
guile-1.8
ii guile-lib
0.1.6Installs guile-lib
ii guile-net-http
0.3.1-1 Installs the net-http scm file
ii guile18-gtk
2.0 guile-gtk-2.0 for guile18
ii libguile-ltdl-1
1.6.8-6.3ubuntu1 Guile's patched version of
libtool's libltdl
I've also noticed that sometimes what the configure error reports
isn't accurate when you look at the log files -- it might be choking
on something else.
On May 12, 2009, at 8:11 AM, hari jayaram wrote:
Hello ,
The jaunty 32 bit build seems to fail ( with subversion revision
2002 as
well)
It seems like based on what Ed Pozharsky wrote in ..its a problem
with guile
in Ubuntu jaunty (9.04) ..
On my 32 bit , 9.04 installation , the build-it-gtk2-simple script
chugs
along fine and then declares the following contradictory message
checking for Clipper... yes
Congratulations, you are using Guile
checking for guile... no
configure: error: guile required but not found
Regardless ..I will try Bill Scots or the CCP4 wiki
methodhttp://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Custom_building_Coot_from_source_code
of
separately compiling all the coot dependencies . But though I would
wrote
in to inquire if there was already a simpler fix.
Thanks
Hari
On Fri, May 8, 2009 at 7:35 PM, Paul Emsley paul.ems...@bioch.ox.ac.uk
wrote:
hari jayaram wrote:
Hi ..I tried a coot subversion (revision 1994) built-it-simple
python on
the newest ubuntu 9.04
The build crashes just after it builds guile and ( 16-coot.txt in
the
build directory ) reads :
checking for Clipper... yes
Congratulations, you are using Guile
checking for guile... no
configure: error: guile required but not found
./build-it-gtk2-simple: line 2742: [: =: unary operator expected
NO need to update libtool
/home/hari/autobuild/ex-charlie_2009-05-08__T20_14_49/coot-0.6-pre-1
make: *** No targets specified and no makefile found. Stop.
This happens only on the new ubuntu (on a 32 bit 9.04 system) .
I was able to build this revision without any problem on Ubuntu
8.04 64
bit
Thanks update_libtool is not set sometimes, so using it as in 1994 is
wrong. I've tweaked the script.
But the problem for you lies above that..
checking for guile... no
configure: error: guile required but not found
Hmm! what went wrong there..?
I'll try to build from scratch on Jaunty myself.
Cheers,
Paul.
Re: [COOT] RSR exploding RNA
On May 5, 2009, at 3:16 PM, CK wrote: Hi all, I am refining a structure that contains RNA. I've added hydrogens in the riding positions to help with maintaining proper geometry during refinement. However, when I go to adjust the model between refinements in coot using Real Space Refine (or even Regularize for that matter) the RNA explodes with atoms going every which way. This didn't happen before I had added in hydrogens (with Molprobity via Reduce). Also, when I Real Space Refine residues from the protein portion, the heavy atoms (C, O, N) behave normally while about half of the riding hydrogens go wandering off. Any particular reason why this might be happening? Hydrogen can be quite explosive. Have you tried helium? But seriously, if the program you used to hydrogenate uses a nomenclature that coot/refmac doesn't expect, this could happen. Also the zero occupancy might be the culprit. However you mentioned that without hydrogens it was hard to maintain proper geometry. This might be a cause for concern, or re-examination of the structure and its density.
Re: [COOT] coot dependency on $LANG?
Could you (or we) set LANG=en_US.US-ASCII in the coot wrapper script? On Apr 29, 2009, at 8:01 AM, Steffen Schmidt wrote: Hi, I experienced a weird error (amino acids are not connected) when setting the environmental variable LANG to de_DE.UTF-8 (on a OS X 10.5 machine). I guess this language setting is screwing up the PDB file parsing since german uses ',' as decimal separator… BW Steffen
Re: [COOT] coot-0.6-pre1-1941 for intel OS X 10.4/10.5
On Mar 29, 2009, at 2:34 AM, Phil Evans wrote: On 29 Mar 2009, at 04:42, William G. Scott wrote: This I hope will address previous grievances: http://tinyurl.com/coot1941 ... except I get a load of errors I didn't have before :-( and no splash screen or icons. The files all seem to be there. Any ideas? I need to find a different line of employment. This one apparently cured the same problem for Ralf that was occurring previously for him. Just to humo(u)r me and perhaps enable diagnosis of the problem once and for all, what version of OS X, X11, and make of computer are you using? Sorry for this. Bill
Re: [COOT] [ccp4bb] coot crashes
On Mar 2, 2009, at 4:25 AM, Vellieux Frederic wrote: Any idea? Is it there? http://www.mail-archive.com/ubuntu-b...@lists.ubuntu.com/msg663049.html
Re: [COOT] python or scheme
As far as learning scheme, My $0.02: From a purely practical standpoint, if, like me, you have limited time, energy and mental capacity, python would probably yield a better investment payback. There are numerous extensions available that make parsing things like pdb files very simple, there is the whole phenix/ cctbx resource you can make use of, and it is probably the most powerful and commonly employed scripting language among scientists (bioinformatics people like perl, for its text processing abilities). The syntax is very clean and straightforward and you don't have to deal with huge piles of dollar signs and parentheses all over the place. Whichever you use, be sure to use an editor that employs an intelligent syntax highlighting mechanism, like vim, or even emacs (if you type with a lisp). On OS X, TextMate is my editor of choice. Here's a site that lists some of the available modules: http://wiki.python.org/moin/NumericAndScientific HTH, Bill
Re: [COOT] coot0.6-pre-1 on FC10
What happens if you turn off all compositing effects? On Feb 23, 2009, at 8:37 AM, David Schwefel wrote: Dear Coot community, I encountered some problems using Coot on fedora core 10. I installed the binaries, and upon starting, the system crashed just in the moment when the Coot window appeared. I have a ATI radeon X1650 graphics card. When I switch from the standard radeon to the ATI fglrx graphics driver, the system does not crash anymore, but Coot quits with the following error message: The program 'coot-real' received an X Window System error. This probably reflects a bug in the program. The error was 'BadRequest (invalid request code or no such operation)'. (Details: serial 661 error_code 1 request_code 143 minor_code 19) (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.) coot-exe: /usr/local/bin/coot-Linux-i386-fedora-10-gtk2-python/bin/ coot-real coot-version: /usr/local/bin/coot-Linux-i386-fedora-10-gtk2-python/bin/coot-real platform: /bin/uname core: #f No core file found. No debugging Any hints how to solve this problem? Best regards and thanks in advance, David
Re: [COOT] python and coot question
On Jan 30, 2009, at 10:50 AM, Nathaniel Echols wrote: the binaries I was using of coot-0.5-pre1 had this problem, while coot-0.5.1-pre1-1661 used the correct interpreter. That sounds like something I made, in which case I am even more puzzled. The interpreter is actually supposed to be coot itself - I don't think /sw/bin/python is going to do you any good, since it doesn't have access to the memory of the running coot process. OK, but somewhere coot is making the decision to use the system's python libraries in sys.path, so I am assuming it can only get these from /usr/bin/python. I think if I can consistently get it to use /sw/bin/python, then at least I will know what I am trying to fix.
Re: [COOT] Glossy_P gtk+2
Convention is to put it in /usr/share/themes but it can go anywhere. You can source it systemwide with /etc/gtk-2.0/gtkrc and the include line should have the absolute path in double quotes Alternatively, you can source the file from ~/.gtkrc-2.0 and it should work. Or if you use gnome, just download the tarball and install the theme by pointing the gnome theme manager to the tarball. Similarly with xfce4. I don't know how it works on KDE. It will change all the gkt+2 stuff, not just coot. On Jan 16, 2009, at 9:36 AM, Stefan Arold wrote: Thank you for your swift reply! Anticipating problems with the space in the name, I had initially changed the directory name to Glossy_P (-no space). However, changing it back, and pointing to it in the way you indicated, does not help... Is there a particular directory where Glossy P needs to be sitting? Or where the .gtkrc-2.0 file (containing the include /usr/share/ themes/Glossy\ P/gtk-2.0/gtkrc) needs to be placed? (I tried ~/, or COOT subdirectories etc and themes) Or did I miss out something in my path? (for COOT it points at the bin directory of the current COOT download) Many thanks for your time and suggestions! Stefan == Stefan T. Arold, PhD Centre de Biochimie Structurale CNRS UMR 5048 - UM 1 - INSERM UMR 554 29 rue de Navacelles 34090 MONTPELLIER Cedex - France email: stefan.ar...@cbs.cnrs.fr Phone: +33 (0)4.67.41.77.02 Fax: +33 (0)4.67.41.79.13 == - Original Message - From: William G. Scott wgsc...@chemistry.ucsc.edu To: COOT@JISCMAIL.AC.UK Sent: Friday, January 16, 2009 6:04 PM Subject: Re: Glossy_P gtk+2 That would be my fault. On Ubuntu, I have this: % more /etc/gtk-2.0/gtkrc include /usr/share/themes/Glossy\ P/gtk-2.0/gtkrc gtk-font-name = Sans 13 The one difference I see is the escaped space rather than the underscore, so verify which you should have. On Jan 16, 2009, at 8:30 AM, Stefan Arold wrote: Dear All, I am using coot 0.5.2 on a PC (i686 Intel(R) Core(TM)2 Duo 2.20GHz GNU/Linux) under mandriva 2008. I tried to install the Glossy_P gtk +2 themes as described in the coot wiki. To get this effect, you need the Glossy_P gtk+2 theme: http://art.gnome.org/download/themes/gtk2/571/GTK2-Glossy_P.tar.gz Edit a file called ~/.gtkrc-2.0 and put into it the following line: include /usr/share/themes/Glossy_P/gtk-2.0/gtkrc However: no effect... I've tried to copy the Glossy_P/gtk-2.0/gtkrc in various places, including the subdirectories 'themes' and 'etc' of my current coot download (coot-Linux-i386-redhat-8.0-gtk1-python). Without effect... any help to gloss my coot would be greatly appreciated! Cheers Stefan
Re: [COOT] coot for 10.4 and 10.5 intel
The only difference should be the version of coot. On Dec 15, 2008, at 10:23 AM, Nathaniel Echols wrote: Hey Bill, this has the correct and complete Python module search paths too (although /usr/local/xtal/coot/share/coot/python is repeated four times, but this doesn't appear to break anything). What's the difference between this and the coot-0.5-pre1 build you sent out on Thursday? thanks, Nat (still no coot_python, but I'm pretty sure that's a different problem.) On Fri, Dec 12, 2008 at 9:40 PM, William Scott wgsc...@chemistry.ucsc.eduwrote: Is this one any better? http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Coot-0.5.1-pre1_revision_1661_for_intel-10.4-10.5 On Fri, December 12, 2008 2:53 am, Valerie Biou wrote: Hi Bill, I installed it this morning and it starts ok. all I tried is SSM, it still crashes. Do you want me to test other things? all the best Valerie William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [COOT] problem in coot installation in ubuntu
Oh, in case anyone is wondering how I did this (and how I screwed it
up), the correct command should have been:
dpkg -S $( ldd /usr/local/xtal/coot/bin/coot-real | awk '{print $3}'
| sort -u | grep -v \( )| cut -f 1 -d : | sort -u | perl -pi -e 's|
\n|\, |g' | dependencies.txt
whereas I first used
dpkg -S $( ldd /usr/local/xtal/coot/bin/coot-real | awk '{print $1}'
| sort -u | grep -v \( )| cut -f 1 -d : | sort -u | perl -pi -e 's|
\n|\, |g' | dependencies.txt
My bad. I needed the third column of the output of ldd to get the
full path of the dynamic library. The first column only reports the
name of the file, and then it wrongly assumed it was in my NX
directory (it wasn't). Coot was properly linked. The list of
dependencies in the debian file was wrong. Fixed now.
( coot_0.5-2_i386.deb ). Again, thanks for catching this.
Bill
On Nov 17, 2008, at 6:57 AM, William G. Scott wrote:
Woops. I didn't see that. I auto-generated the list of
dependencies from the output of ldd on the coot binary, upon which I
then used dpgk -S to find the corresponding packages. For some
reason it generated this falsely (the library is also present, but
ldd does not report coot linking anything with NX in the path).
Sorry, I will edit this out.
Thanks for testing.
Bill
On Nov 17, 2008, at 3:16 AM, Mark Brooks wrote:
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
Re: [COOT] problem in loading icons
Hi Enrico: I have this: % dpkg -S svg_loader.so librsvg2-gtk: /sw/lib/gtk-2.0/2.10.0/loaders/svg_loader.so The package that provides this is librsvg2-gtk, which should be a coot dependency. Could you please check, and maybe try reinstalling it, ie. fink reinstall librsvg2-gtk and let me know what happens? Many thanks in advance, and also many thanks to Charles Ballard for pointing this out. Bill On Nov 17, 2008, at 12:49 PM, Ballard, CC (Charles) wrote: Hi Enrico For some reason the pixbuf.loaders file does not contain the information about the svg_loader. This is normally achieved by running gdk-pixbuf-query-loaders and piping the output to the pixbuf.loaders file (use find to locate it). To confirm that you have the svg library setup in gdk in the first place try and locate the svg_loader.la file (in my case - none fink - it is in lib/gtk-2.0/2.10.0/loaders ). gdk-pixbuf-query-loaders will have a manual page if more info is required. If all else fails, there is a bundle of coot 0.5 at http://www.ccp4.ac.uk/download/downloadman.php Charles -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:[EMAIL PROTECTED] On Behalf Of Enrico Malito Sent: 17 November 2008 16:09 To: COOT@JISCMAIL.AC.UK Subject: [COOT] problem in loading icons Hello, I was wondering if anybody observed this before. When I start coot I get this messages (a long list of errors for the whole content of the folder /sw/share/coot/pixmaps/): Error loading icon: Couldn't recognize the image file format for file '/sw/share/coot/pixmaps/add-alt-conf.svg' Error loading icon: Couldn't recognize the image file format for file '/sw/share/coot/pixmaps/add-peptide-1.svg' ... ... Error loading icon: Couldn't recognize the image file format for file '/sw/share/coot/pixmaps/undo-1.png' Error loading icon: Couldn't recognize the image file format for file '/sw/share/coot/pixmaps/unknown-blob.png' initalize graphics molecules...done. and no icons are loaded in the right bar of coot, only grey boxes (see attach). This is 0.5.1-pre-1 installed through fink on OSX 10.5.5, and those icons files are actually there (in /sw/share/coot/pixmaps/) and seem oK. Thanks much in advance for any hints. EM
Re: [COOT] problem in loading icons
Another idea: If you have $DYLD_LIBRARY_PATH assigned, try unsetting it before invoking coot, i.e., issue DYLD_LIBRARY_PATH= ; coot On Nov 17, 2008, at 8:09 AM, Enrico Malito wrote: Hello, I was wondering if anybody observed this before. When I start coot I get this messages (a long list of errors for the whole content of the folder /sw/share/coot/pixmaps/): Error loading icon: Couldn't recognize the image file format for file '/sw/share/coot/pixmaps/add-alt-conf.svg' Error loading icon: Couldn't recognize the image file format for file '/sw/share/coot/pixmaps/add-peptide-1.svg' ... ... Error loading icon: Couldn't recognize the image file format for file '/sw/share/coot/pixmaps/undo-1.png' Error loading icon: Couldn't recognize the image file format for file '/sw/share/coot/pixmaps/unknown-blob.png' initalize graphics molecules...done. and no icons are loaded in the right bar of coot, only grey boxes (see attach). This is 0.5.1-pre-1 installed through fink on OSX 10.5.5, and those icons files are actually there (in /sw/share/coot/pixmaps/) and seem oK. Thanks much in advance for any hints. EM Picture 1.png
Re: [COOT] regarding installing coot via fink
Hi Arnab: Unfortunately, sometimes there are glitches installing some of these packages that are dependencies, and I'm not up on each of the 100 fink dependencies that coot has. The best thing is to try a second time, and if that doesn't work, issue fink describe packagename and it will give you an email address for the package maintainer. Also there is a fink user's email list with very knowledgeable people on it, and it is probably the fastest way to get a problem fixed. Bill On Oct 15, 2008, at 5:27 PM, Arnab Bhattacharjee wrote: While installing coot via fink I am repeatedly getting this msg /sw/bin/dpkg-lockwait -r fink-buildlock-gnome-vfs2-unified-2.20.1-2 (Reading database ... 45318 files and directories currently installed.) Removing fink-buildlock-gnome-vfs2-unified-2.20.1-2 ... Failed: phase compiling: gnome-vfs2-unified-2.20.1-2 failed i tried to rebuid gnome-vfs2 manually as well by the rebuild and install command in finkcoudn't do it Any tips plz? Thanks and Regards -- ARNAB BHATTACHARJEE Dept. of Bacteriology and Immunology SERO Group, Haartman Institute Haartmaninkatu 3 University of Helsinki FIN-00014 HELSINKI Tel. +358-9-191 26385 Fax. +358-9-191 26382 Structural Biology and Biophysics Macromolecular X-ray Crystallography Group Institute of Biotechnology. Biocenter: 3, Viikinkari 1 University of Helsinki FIN-00790 HELSINKI Tel. +358-9-191 58922 Fax +358-9-191 59940 On 14 Oct 2008, at 20:37, William Scott wrote: Sorry, I just realized that quick-fix won't work. Instead, edit the file /sw/etc/apt/sources.list take out the kotoushu lines and put in the three lines shown on this page: http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Sources.list_for_10.5_intel_only i.e., deb http://sage.ucsc.edu/fink_intel_10.5_only stable main crypto deb http://sage.ucsc.edu/fink_intel_10.5_only unstable main crypto deb http://sage.ucsc.edu/fink_intel_10.5_only local main Then issue fink selfupdate-rsync sudo apt-get update fink -b update-all On Oct 14, 2008, at 9:43 AM, William G. Scott wrote: Dear Arnab: kotoushu used to host 10.4 intel fink debians, but it is no longer available. Since you are using 10.5, the easiest thing to do is this: sudo perl -pi -e 's|kotoushu|sage|g' /sw/etc/apt/sources.list if you need further details: http://tinyurl.com/fink-precompiled Also make sure you have a recent version of X11.app (ie 2.3.1): http://xquartz.macosforge.org/trac/wiki Bill On Oct 14, 2008, at 7:30 AM, Arnab Bhattacharjee wrote: Hi Bill, This is in regard of installing coot in my Mac laptop (leopard, 10.5). I installed the older version of coot via fink. Now I tried to install the latest version directly taking the pre compiled binaries first and then it didn't worked. Then I tried to install it via fink again. But repeatedly its saying Err http://kotoushu.ucsc.edu unstable/main opensp4-shlibs 1.5.1-1006 Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). - connect (61 Connection refused) Err http://kotoushu.ucsc.edu unstable/main opensp4 1.5.1-1006 Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). - connect (61 Connection refused) Err http://kotoushu.ucsc.edu unstable/main opensp4-dev 1.5.1-1006 Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). - connect (61 Connection refused) Err http://kotoushu.ucsc.edu unstable/main sgml-entities-iso8879 1986-4 Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). - connect (61 Connection refused) Err http://kotoushu.ucsc.edu unstable/main xft2-dev 2.1.2-5 So can u give me some tips of how to come out of the problem. I actually tried to overwrite the earlier version of coot and hence the older version doesn't work any more. Will be really helpful if u can bail me out of the situation. Best regards Arnab Thanks and Regards -- ARNAB BHATTACHARJEE Dept. of Bacteriology and Immunology SERO Group, Haartman Institute Haartmaninkatu 3 University of Helsinki FIN-00014 HELSINKI Tel. +358-9-191 26385 Fax. +358-9-191 26382 Structural Biology and Biophysics Macromolecular X-ray Crystallography Group Institute of Biotechnology. Biocenter: 3, Viikinkari 1 University of Helsinki FIN-00790 HELSINKI Tel. +358-9-191 58922 Fax +358-9-191 59940
Re: [COOT] Nucleotide Builder
I agree, but why do you want to build B-form RNA? On Oct 10, 2008, at 8:48 AM, Daniel Holloway wrote: I'm using the 'Ideal DNA/RNA...' function. When I try to build A- form RNA, I get what I want. When I ask for B-form RNA, I get DNA! Looks like something to fix... Many thanks
Re: [COOT] Nucleotide Builder
Oh, I thought you had discovered a new form of RNA. You might want to use phenix's elbow builder module. Then you will have a cif file for the ligand too. On Oct 10, 2008, at 9:36 AM, Daniel Holloway wrote: I'm just interested in taking one residue (a 5'-AMP or 3',5'-ADP with the ribose in the C2'-endo conformation) and using it as the basis for a novel ligand. On Fri, 10 Oct 2008 09:13:57 -0700, William G. Scott [EMAIL PROTECTED] wrote: I agree, but why do you want to build B-form RNA? On Oct 10, 2008, at 8:48 AM, Daniel Holloway wrote: I'm using the 'Ideal DNA/RNA...' function. When I try to build A- form RNA, I get what I want. When I ask for B-form RNA, I get DNA! Looks like something to fix... Many thanks
[COOT] embarrassing question
Hi Citizens: I can't remember who was working on pre-compiling the OS X 10.4X intel coot. Could someone remind me? Thanks, and sorry. Bill
Re: [COOT] CNS coordinate in COOT
run the pdb file through ccp4's pdbset, which will canonicalize it (if that is a word). On Oct 5, 2008, at 5:59 PM, Masaki UNNO wrote: Hi Colleagues I am using CNS for structural refinements. I have installed COOT_0.5 but I think the new version of COOT cannot display CNS coordinate properly. It did not display the color by atom and secondly structures. How can I display the CNS coordinate by atom or so? The CNS version is 1.2. Best regards. - Masaki Unno, PhD. Inst. of Multidisciplinary Research for Advanced Materials, Tohoku University 2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan Tel: +22-217-5117 Fax: +22-217-5118
[COOT] OS X 10.4.X G4 ppc libgmp.3.dylib
Does anyone have a copy of libgmp.3.dylib from OS X 10.4.X built on a G4 ppc, preferably with a single processor, that works with coot? If so could you please email it to me? Thanks. Bill
