Re: [COOT] (Re)beginner question about coot binary version on Linux Ubuntu
Thanks Paul for both messages. Thanks a ton for a summary of the various projects underway. I’m working on the build-it script on the Linux side while I figure out a ccp4 full license for my “self learning” small use. The build it script runs aground with some numpy libraries missing , even though I had python-numpy-dev..but i’ll keep at it. In the case of openssl missing errors..it was certainly installed and pointed to by the LD_LIBRARY_PATH..but it probably was a version mismatch because I had different version Hari On Wed, May 24, 2023 at 3:26 PM Paul Emsley wrote: > > On 24/05/2023 14:24, hari jayaram wrote: > > > CAUTION: This email originated from outside of the LMB. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > *.-owner-c...@jiscmail.ac.uk-.* > > Hi All > I am making some progress--but still cant get any of the binaries working > > I have the openssl libraries installed but still get the following error > with coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python > > Thanks for your help > Hari > > > > > "hari@LT-Hari-Linux:/usr/lib/x86_64-linux-gnu$ > ~/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/bin/coot > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: > libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: > /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: > /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by > /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) > > > It is not clear to me if libcrypto is not installed (in which case you > should install it) or is a more modern version than my binary expects (in > which case, there is no hope for the binary that I have built (you might > like to try the build-it script)). > > Paul. > > > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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] (Re)beginner question about coot binary version on Linux Ubuntu
Hi All I am making some progress--but still cant get any of the binaries working I have the openssl libraries installed but still get the following error with coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python Thanks for your help Hari "hari@LT-Hari-Linux:/usr/lib/x86_64-linux-gnu$ ~/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/bin/coot /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) . -- Coot crashed - trying to diagnose - ldd -r on guile gives: linux-vdso.so.1 (0x7ffdbdfae000) libguile.so.17 => /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libguile.so.17 (0x7f6d85ccc000) libc.so.6 (0x7f6d85aa4000) libgmp.so.10 => /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libgmp.so.10 (0x7f6d85a2b000) libcrypt.so.1 (0x7f6d859ef000) libm.so.6 (0x7f6d85908000) libltdl.so.3 => /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libltdl.so.3 (0x7f6d858fd000) libpthread.so.0 (0x7f6d858f8000) /lib64/ld-linux-x86-64.so.2 (0x7f6d85dd2000) libdl.so.2 (0x7f6d858f3000) Guile 1.8.8 Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation Guile may be distributed under the terms of the GNU General Public Licence; certain other uses are permitted as well. For details, see the file `COPYING', which is included in the Guile distribution. There is no warranty, to the extent permitted by law. catching the crash log: coot-exe: "/home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin" /usr/bin/ls -rwxr-xr-x 1 hari hari 423402112 Mar 10 2022 /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin coot-version: /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: libcrypto.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/libexec/coot-bin: /lib/libssl.so.1.1: version `OPENSSL_1_1_0' not found (required by /home/hari/coot-Linux-x86_64-ubuntu-20.04.4-gtk2-python/lib/libcurl.so.4) platform: /usr/bin/uname Linux LT-Hari-Linux 5.15.0-56-generic #62-Ubuntu SMP Tue Nov 22 19:54:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux core: #f No core file found. No debugging " On Tue, May 23, 2023 at 9:13 PM hari jayaram wrote: > Hi All > I want to get back to using coot to build some models after a gap of 8 > years. > > I have access to a Linux laptop and can put any OS version on it. > > I was wondering what the easiest way forward is —get the most recent > Ubuntu and pull the latest binary ( 0.9.8.6 with binary for 20.04) or put > the iso that coot was built for (20.04) on the laptop and start using it. > > > Asking because I just tried using the newest mint distro ( Mint 21.1 > Vera) and one of the binaries > (coot-Linux-x86_64-scientific-linux-7.6-gtk2-python) and it runs aground > without OpenSSL and ldap.so versions are being mismatched. When I switched > to coot-0.9.8-binary-Linux-x86_64-ubuntu-20.04.4-python-gtk2 then it > complained of a version mismatch for libssl.so.1.1 > > Thanks for your help in advance > > > Hari > > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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/
[COOT] (Re)beginner question about coot binary version on Linux Ubuntu
Hi All I want to get back to using coot to build some models after a gap of 8 years. I have access to a Linux laptop and can put any OS version on it. I was wondering what the easiest way forward is —get the most recent Ubuntu and pull the latest binary ( 0.9.8.6 with binary for 20.04) or put the iso that coot was built for (20.04) on the laptop and start using it. Asking because I just tried using the newest mint distro ( Mint 21.1 Vera) and one of the binaries (coot-Linux-x86_64-scientific-linux-7.6-gtk2-python) and it runs aground without OpenSSL and ldap.so versions are being mismatched. When I switched to coot-0.9.8-binary-Linux-x86_64-ubuntu-20.04.4-python-gtk2 then it complained of a version mismatch for libssl.so.1.1 Thanks for your help in advance Hari To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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] Which Linux distribution supports building Coot 1.0.x?
Thanks Paul I’ll also try and find the appropriate lines from build script to build an upgraded clipper in the meantime. Guessing this is the 0.9.x series build script you are referring to? Thanks again Hari On Wed, Jun 29, 2022 at 5:37 PM Paul Emsley wrote: > > This is primarily my mistake. I now think that coot's configure should > check for the version of clipper that has top8000. > > If it doesn't find that clipper, then Coot's configure should fail. > > You should never get to the make stage. > > I will take a look at what I need to do to make that happen (because, > clearly, it isn't). > > A few days. > > Paul. > > > > On 27/06/2022 03:12, Paul Emsley wrote: > > > That clipper is old clipper. You need the clipper from the build script. > > Paul. > > > > On 27/06/2022 03:10, hari jayaram wrote: > > Dear Paul and the coot community > It's been 6 years since I posted on any coot forum . I saw the exciting > news around coot-1 and am itching to dive back in. > > I am trying to compile coot-1 on Ubuntu 20.04 > > After installing a series of dependencies, which I can gladly report back > to you on...the build started without any issues. It however stopped with > this error --see below > I got all the libraries including the clipper libraries from Ubuntu ( sudo > apt-get install libclipper-dev) > > I wonder how to proceed past this. > > Thanks a tonne for your help > Hari > > > """ > /bin/bash ../libtool --tag=CXX --mode=compile g++ > -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1\" > -DPACKAGE_STRING=\"coot\ 1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" > -DPACKAGE=\"coot\" -DVERSION=\"1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 > -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 > -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 > -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_CXX11=1 > -DHAVE_CXX_THREAD=1 -DHAVE_PYTHON=\"3.8\" -DHAVE_BOOST=/\*\*/ > -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include > -DMMDB_HAS_LINK_DISTANCE -fopenmp -DPKGDATADIR='"/usr/local/share/coot"' > -DUSE_LIBPNG=1 -I/usr/include/libpng16 -g -O2 -Wall -Wno-unused > -std=c++11 -MT residue_by_phi_psi.lo -MD -MP -MF > .deps/residue_by_phi_psi.Tpo -c -o residue_by_phi_psi.lo > residue_by_phi_psi.cc > libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" > -DPACKAGE_VERSION=\"1\" "-DPACKAGE_STRING=\"coot 1\"" > -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" > -DVERSION=\"1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 > -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 > -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 > -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 > -DHAVE_PYTHON=\"3.8\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I. > -I.. -DHAVE_GSL -I/usr/include -DMMDB_HAS_LINK_DISTANCE -fopenmp > -DPKGDATADIR=\"/usr/local/share/coot\" -DUSE_LIBPNG=1 > -I/usr/include/libpng16 -g -O2 -Wall -Wno-unused -std=c++11 -MT > residue_by_phi_psi.lo -MD -MP -MF .deps/residue_by_phi_psi.Tpo -c > residue_by_phi_psi.cc -fPIC -DPIC -o .libs/residue_by_phi_psi.o > residue_by_phi_psi.cc: In member function ‘void > coot::residue_by_phi_psi::init_phi_psi_plot()’: > residue_by_phi_psi.cc:869:37: error: ‘All2’ is not a member of > ‘clipper::Ramachandran’ > 869 |rama.init(clipper::Ramachandran::All2); > | ^~~~ > residue_by_phi_psi.cc:871:41: error: ‘Pro2’ is not a member of > ‘clipper::Ramachandran’ > 871 |rama_pro.init(clipper::Ramachandran::Pro2); > | ^~~~ > make[1]: *** [Makefile:1324: residue_by_phi_psi.lo] Error 1 > make[1]: Leaving directory '/home/hari-verve/coot-1/ligand' > make: *** [Makefile:723: all-recursive] Error 1 > """ > > On Mon, Jun 13, 2022 at 4:56 PM Paul Emsley > wrote: > >> On 13/06/2022 18:40, Giacomo Fiorin wrote: >> > FYI while I'm still going through dependencies from Ubuntu 20.04 >> packages, I also tried CentOS 7 again by installing guile-devel to >> circumvent the script's auto-build of GUILE, and it builds Coot >> successfully. However, when I launch it I see a splash screen and the >> following messages, after which Coot exits w
Re: [COOT] Which Linux distribution supports building Coot 1.0.x?
Dear Paul and the coot community It's been 6 years since I posted on any coot forum . I saw the exciting news around coot-1 and am itching to dive back in. I am trying to compile coot-1 on Ubuntu 20.04 After installing a series of dependencies, which I can gladly report back to you on...the build started without any issues. It however stopped with this error --see below I got all the libraries including the clipper libraries from Ubuntu ( sudo apt-get install libclipper-dev) I wonder how to proceed past this. Thanks a tonne for your help Hari """ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1\" -DPACKAGE_STRING=\"coot\ 1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_PYTHON=\"3.8\" -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -DMMDB_HAS_LINK_DISTANCE -fopenmp -DPKGDATADIR='"/usr/local/share/coot"' -DUSE_LIBPNG=1 -I/usr/include/libpng16 -g -O2 -Wall -Wno-unused -std=c++11 -MT residue_by_phi_psi.lo -MD -MP -MF .deps/residue_by_phi_psi.Tpo -c -o residue_by_phi_psi.lo residue_by_phi_psi.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1\" "-DPACKAGE_STRING=\"coot 1\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_PYTHON=\"3.8\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -DMMDB_HAS_LINK_DISTANCE -fopenmp -DPKGDATADIR=\"/usr/local/share/coot\" -DUSE_LIBPNG=1 -I/usr/include/libpng16 -g -O2 -Wall -Wno-unused -std=c++11 -MT residue_by_phi_psi.lo -MD -MP -MF .deps/residue_by_phi_psi.Tpo -c residue_by_phi_psi.cc -fPIC -DPIC -o .libs/residue_by_phi_psi.o residue_by_phi_psi.cc: In member function ‘void coot::residue_by_phi_psi::init_phi_psi_plot()’: residue_by_phi_psi.cc:869:37: error: ‘All2’ is not a member of ‘clipper::Ramachandran’ 869 |rama.init(clipper::Ramachandran::All2); | ^~~~ residue_by_phi_psi.cc:871:41: error: ‘Pro2’ is not a member of ‘clipper::Ramachandran’ 871 |rama_pro.init(clipper::Ramachandran::Pro2); | ^~~~ make[1]: *** [Makefile:1324: residue_by_phi_psi.lo] Error 1 make[1]: Leaving directory '/home/hari-verve/coot-1/ligand' make: *** [Makefile:723: all-recursive] Error 1 """ On Mon, Jun 13, 2022 at 4:56 PM Paul Emsley wrote: > On 13/06/2022 18:40, Giacomo Fiorin wrote: > > FYI while I'm still going through dependencies from Ubuntu 20.04 > packages, I also tried CentOS 7 again by installing guile-devel to > circumvent the script's auto-build of GUILE, and it builds Coot > successfully. However, when I launch it I see a splash screen and the > following messages, after which Coot exits with error. > > > > I'll try to move forward with Ubuntu 20.04, but if support for > RHEL/CentOS 7 is restored it would be very helpful. Thanks! > > > Try setting your path so that > > /data/local/Fiorin/build/autobuild/coot-Linux-x86_64-centos-7-gtk3/bin is > the first element > > Paul. > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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&A=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] broken loggraph on 64 bit redhat: new style refmac graph popup after refmac from inside coot?
Thanks a lot Bernhard.
I could not get this to work on Redhat Enterprise 6.5 and have switched to
not running refmac from inside coot as a stop gap.
It will be great to have the qt output option directly from inside coot..I
will gladly pull from svn and test it out.
Thanks a tonne
Hari
On Wed, Apr 23, 2014 at 1:54 AM, Bernhard Lohkamp wrote:
>
> Sorry, didnt see this earlier... catching up with a massive backlog on
> emails.
> I dont have any solution to your loggraph problem, but Coot should
> certainly allow (by default and if available) the use of qtrview. I put
> this on my list to do (somewhere on the top ;-) ).
>
> B
>
>
> On 05/04/2014 15:04, hari jayaram wrote:
>
>> Hi all,
>> I like running my refmac from inside coot and having the loggraph blt
>> graphs popup on completion.
>> loggraph graph pop ups seem broken on 64 bit redhat enterprise running
>> ccp4 6.3 and ccp4 6.4 , both 64 bit versions. The window for the graph
>> pops up and then crashes with an error complaining of the loggraph.tcl
>> script( see below).
>>
>> This script nor associated scripts have not changed in ccp4 for a while,
>> and everything works on 64 bit Ubuntu, so I am scared the error may like
>> with some redhat component.
>> I tried to compile a "native" blt instead of using the ccp4 supplied one
>> to see if that fixed things. Digging through the blt forums etc it seems
>> that many are abandoning blt to something like a replacement called
>> wize. Also judging from the forums several things in the blt 2.4 and
>> older seem to have issues with newer tk flavors like 8.5.
>>
>> Regardless , given all this , are there any ways to auto popup the new
>> style qt based graphs when running refmac from within coot upon
>> completion.
>>
>> Sorry I am cross posting to coot, ccp4bb.
>>
>> thanks for your help in advance.
>> hari
>>
>> the error I see in refmac : view log graphs OR in coot on refmac
>> completion says:
>>
>> "Error in startup script: syntax error in expression "10 11 12 + 12":
>> extra tokens at end of expression
>> while executing
>> "expr [string trim $ele] + $data(NCOLUMNS) "
>> (procedure "extract_tables_from_GRAPH" line 44)
>> invoked from within
>> "extract_tables_from_$filetype $input $arrayname"
>> (procedure "extract_tables_from_file" line 31)
>> invoked from within
>> "extract_tables_from_file $system(SCRIPT) $system(FORMAT) data"
>> invoked from within
>> "if { $system(SCRIPT) != "" } {
>>if { ![ElementExists system FORMAT] || $system(FORMAT) == "" } {
>> set system(FORMAT) [GetFileFormat $system(SCRI..."
>> (file
>> "/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl"
>> line 2324)
>> invoked from within
>> "source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]"
>> (file
>> "/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl" line
>> 83)
>> "
>>
>>
>>
> --
> ***
>
> Dr. Bernhard Lohkamp
> Associate Professor/Docent
> Div. Molecular Structural Biology
> Dept. of Medical Biochemistry and Biophysics (MBB)
> Karolinska Institutet
> S-17177 Stockholm
> Sweden
>
> phone: (+46) 08-52487651
> fax: (+46) 08-327626
> email: bernhard.lohk...@ki.se
>
[COOT] broken loggraph on 64 bit redhat: new style refmac graph popup after refmac from inside coot?
Hi all,
I like running my refmac from inside coot and having the loggraph blt
graphs popup on completion.
loggraph graph pop ups seem broken on 64 bit redhat enterprise running ccp4
6.3 and ccp4 6.4 , both 64 bit versions. The window for the graph pops up
and then crashes with an error complaining of the loggraph.tcl script( see
below).
This script nor associated scripts have not changed in ccp4 for a while,
and everything works on 64 bit Ubuntu, so I am scared the error may like
with some redhat component.
I tried to compile a "native" blt instead of using the ccp4 supplied one to
see if that fixed things. Digging through the blt forums etc it seems that
many are abandoning blt to something like a replacement called wize. Also
judging from the forums several things in the blt 2.4 and older seem
to have issues with newer tk flavors like 8.5.
Regardless , given all this , are there any ways to auto popup the new
style qt based graphs when running refmac from within coot upon completion.
Sorry I am cross posting to coot, ccp4bb.
thanks for your help in advance.
hari
the error I see in refmac : view log graphs OR in coot on refmac completion
says:
"Error in startup script: syntax error in expression "10 11 12 + 12": extra
tokens at end of expression
while executing
"expr [string trim $ele] + $data(NCOLUMNS) "
(procedure "extract_tables_from_GRAPH" line 44)
invoked from within
"extract_tables_from_$filetype $input $arrayname"
(procedure "extract_tables_from_file" line 31)
invoked from within
"extract_tables_from_file $system(SCRIPT) $system(FORMAT) data"
invoked from within
"if { $system(SCRIPT) != "" } {
if { ![ElementExists system FORMAT] || $system(FORMAT) == "" } {
set system(FORMAT) [GetFileFormat $system(SCRI..."
(file
"/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/loggraph/loggraph.tcl"
line 2324)
invoked from within
"source [file join $env(CCP4I_TOP) loggraph loggraph.tcl]"
(file
"/home/yong.tang/ccp4_root/ccp4-6.4.0/share/ccp4i/bin/loggraph.tcl" line 83)
"
Re: [COOT] coot operator for SYMGEN - Make new molecule from symop- pisa interface?
Thanks a tonne Paul.. That is exactly what I was looking for. It works like magic :-) Hari On Thu, Oct 24, 2013 at 9:38 AM, Paul Emsley wrote: > On 23/10/13 11:48, hari jayaram wrote: > >> I have a question about the expanded syminfo labels in coot and the menu >> item : Extensions-Modelling-New Molecule from symop. >> >> I have a dimer in the asymmetric unit in which the two molecules that >> phaser picked as the solution do not share any contact area . I want to put >> chain A together with a symmetry generated B molecule. >> >> > Hi Hari, > > You want to move the B chain so that it is in a symmetry-related position > (that is close to the A chain)? > > Centre on an atom in the symmetry-related B chain (where you want the B > chain to be) > Extensions -> Modelling -> Symm Shift Reference Chain Here. > > Paul > >
[COOT] coot operator for SYMGEN - Make new molecule from symop- pisa interface?
I have a question about the expanded syminfo labels in coot and the menu item : Extensions-Modelling-New Molecule from symop. I have a dimer in the assymetric unit in which the two molecules that phaser picked as the solution do not share any contact area . I want to put chain A together with a symmetry generated B molecule. In my case the molecule that "should" represent B with a maximal interface with A has the expanded symmetry label in coot -X , Y + 1/2, -Z + (1 -1 1) & (1 0 0 ) I however cannot use this label in "get new molecule from symop" to give me the sym-mate with the maximum contact area because the translation is off. I am a little bad at visualizing the matrix operations to edit the matrix to get the right sym-mate. In the past I have done this in pymol where I use the "Action-generate- symmetry around a radius-100" and then gone hunting through the sym-mates pymol generates till I get the right one. My question is : Is there a way to accomplish this within coot..or am I not using the symop label properly. I also know the online PISA ebi web interface writes out the correct "B" molecule which maximizes the A-B interface. I could not get the ccp4 provided PISA to output the same --at least using the default ccp4i settings for PISA. Thanks Hari
[COOT] mmcif output for custom ligand from "Edit Restraints" not compatible with Refmac outside of coot?
Hi all, When I build a custom ligand using the coot Ligand Builder (0.7.1-pre (revision 4650) [with guile 1.8.8 embedded] [with python 2.7.3 embedded]). Coot then runs cprodrg and generates restraints which I can use inside of coot to do all my refinements and even run refmac from within coot. When I however write out those restraints from coot using --Edit- Restraints - Pick DRG - save as mmcif and use the generated cif with refmac (CCP4 6.3: Refmac_5.7.0032) I get an error in the refmac log( see below) Is there some conversion I need to do to the coot saved mmcif file to be able to use it inside refmac. Thanks Hari refmac log excerpt # " I am reading library. Please wait. mon_lib.cif No match for atom ID CAD" subtracting one character No match for atom ID CAD subtracting one character ERR: item _chem_comp_atom.comp_id :-0.022 not found in the monomer list BLOCK :data_comp_DRG IERR =1 There is an error. See above" (truncated) The mmcif file looks like this data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level DRG DRG "DRG " non-polymer 38 20 "." data_comp_DRG loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge DRG CLAI CL CL -0.03901 DRG " CAD" C CR6 -0.022 DRG " CAC" C CR6 0.152 DRG " OAG" O O-0.4321 DRG " NAB" N NR6 0.011 (truncated) The atom names are what are in the PDB fie
Re: [COOT] Coot update refmac output map as map to use for real-space refinement after each run
Thanks Bernhard.. I replaced the refmac.scm from r4648 to the one from my running coot installation and it did the trick.Refmac now updates the active map for refinement to the one it calculates. I did: cp /home/hari/coot-read-only//scheme/refmac.scm /home/hari/autobuild/coot-Linux-x86_64-ubuntu-10.04.4-gtk2-python/share/coot/scheme/refmac.scm On a related note..I do have the following setting (set-keep-map-colour-after-refmac 1) in my .coot file , but it does not seem to be getting picked up and the refmac produced map color does change after the run and the . I am running coot version 0.7.1-pre (revision 4549) [with guile 1.8.8 embedded] [with python 2.7.0 embedded] My setting /home/hari/.coot reads.. (set-keep-map-colour-after-refmac 1) Any ideas on what I am doing wrong. Thanks again Hari On Tue, May 21, 2013 at 5:31 AM, Bernhard Lohkamp wrote: > > Hi Hari, > > sorry for getting back late. There was indeed a bug (in the scheme > scripting). This is fixed in r4647 (just downloading refmac.scm from the > repository should be ok). > > B > > > Hi all, > > I generally run refmac from inside coot. > > > > The "older" coot version would automatically pick the newest maps that > > resulted from refmac as the map to use for refinement..so it would go > > from one FWT map (say map 0) to the newest FWT (map 2) map that > > resulted after refmac.. > > > > However the auto picking of the newest map is no longer happening > > > > Is there someplace in the .coot settings file I can use to set the old > > coot behavior and I am hoping that there is a setting that will pick the > > newest map as the one to be used. > > > > Thanks for your help > > > > Hari > > > > > > > -- > *** > > Dr. Bernhard Lohkamp > Assistant Professor > Div. Molecular Structural Biology > Dept. of Medical Biochemistry and Biophysics (MBB) > Karolinska Institutet > S-17177 Stockholm > Sweden > > phone: (+46) 08-52487651 > fax: (+46) 08-327626 > email: bernhard.lohk...@ki.se >
[COOT] Coot update refmac output map as map to use for real-space refinement after each run
Hi all, I generally run refmac from inside coot. The "older" coot version would automatically pick the newest maps that resulted from refmac as the map to use for refinement..so it would go from one FWT map (say map 0) to the newest FWT (map 2) map that resulted after refmac.. However the auto picking of the newest map is no longer happening Is there someplace in the .coot settings file I can use to set the old coot behavior and I am hoping that there is a setting that will pick the newest map as the one to be used. Thanks for your help Hari
Re: [COOT] Molprobity multicriterion coot charts dont highlight last clicked button in Ubuntu 12.04
Thanks Paul, For now I will grin and bear it since I dont see myself reverting to an older gtk. > I guess it's easier to just move your mouse back over that window (to refocus it). I guess another painful thing in Ubuntu 12.04 with Unity is that "Focus follows mouse" requires a gconf setting ..somehow in my case I cannot get focus follows mouse to work.. Regardless even if I did setup "focus follows mouse"..once I click on the Ubuntu model..in this new GTK the molprobity window would lose the blue/orange ring indicating which button was last active/clicked. On an unrelated note...I am also seeing random slowdowns If I have a few more opengl applications running with one or two java sessions going with Ubuntu 12.04 and the 310.14 nvidia driverdespite having a $2000 graphics card...never was a problem with the 10.04 and non-compiz Ubuntu.. Serves me right for upgrading to 12.04... Thanks for your help Hari On Fri, Apr 5, 2013 at 8:29 AM, Paul Emsley wrote: > On 04/02/2013 09:04 PM, hari jayaram wrote: > >> Hello, >> I auto-upgraded my system to Ubuntu 12,04 and my old coot setup ( from >> 10.04) works just fine on the new system . >> >> There is just one problem in that the coot multicriterion charts >> generated by Molrpobity no longer behave the same way . >> >> When I read in a scheme or python based Molprobity multi-chart..clicking >> on a button does take me to the relevant section of the model..The button >> does have an orange ring indicating it was pressed..but the moment I click >> the mouse on the coot model graphics window ..the orange ring dissapears >> and so I dont know which button I had pressed last >> > > OK, I just tried this and it works the same for me (except I have a blue > highlighting). > > > and conseqeuntly it is very hard to know which ones done and which ones >> are yet to do. >> > > Yes. > > > >> This seems like a new gtk version >> > > Yes, it does. > > > or something else thats causing this behavior. >> > > I would guess not. > > > >> Should I just re-compile coot or is there an OS or coot setting that will >> fix the "issue" >> > > I doubt very much that that would fix things (except if you used an old > version of gtk+ (and that brings its own can of worms). I don't know if > it's possible to "fix" - it may well be that the authors of gtk+ think this > is an improvement. > > I guess it's easier to just move your mouse back over that window (to > refocus it). > > Paul > >
[COOT] Molprobity multicriterion coot charts dont highlight last clicked button in Ubuntu 12.04
Hello, I auto-upgraded my system to Ubuntu 12,04 and my old coot setup ( from 10.04) works just fine on the new system . There is just one problem in that the coot multicriterion charts generated by Molrpobity no longer behave the same way . When I read in a scheme or python based Molprobity multi-chart..clicking on a button does take me to the relevant section of the model..The button does have an orange ring indicating it was pressed..but the moment I click the mouse on the coot model graphics window ..the orange ring dissapears and so I dont know which button I had pressed last and conseqeuntly it is very hard to know which ones done and which ones are yet to do. This seems like a new gtk version or something else thats causing this behavior. Should I just re-compile coot or is there an OS or coot setting that will fix the "issue" Thanks hari
Re: [COOT] Building subversion coot on Ubuntu 12.10 64 bit
Sorry Paul .. Didnt understand your suggestion. In which makefile do I have to move the -ldl after -lpython2.7 I checked out tag 4546 and not I get a different error "Py_Initialize" , "PySys_SetArgv" not declared in scope. ( see bottom of his email) I guess these also have to do with python libs. How do I get around this new error. I know you are moving the source tree over to Cambridge from Oxford and the build script looks for the prerelease server at the URL below..but that returns a 404. I commented it out to get it built till the error below. Also reverting to 4454 I cannot reproduce the error message from yesterday. Sorry for trying to build it while it is still in mid-migration. Thanks for your help Paul and Tim Hari Commented this URL out #pre_release_server_dir= http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/pre-releases/ Error I am getting with 4456 g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7.1-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry -I../coot-utils -I../utils -I/home/ubuntu/autobuild/coot-pre-release-gtk2-python/include -DHAVE_GOOCANVAS -I/home/ubuntu/autobuild/coot-pre-release-gtk2-python/include/goocanvas-1.0 -pthread -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/home/ubuntu/autobuild/coot-pre-release-gtk2-python/include -I/home/ubuntu/autobuild/coot-pre-release-gtk2-python/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/home/ubuntu/autobuild/coot-pre-release-gtk2-python/share/coot"' -g -O -MT lbg-callbacks-outer.o -MD -MP -MF .deps/lbg-callbacks-outer.Tpo -c -o lbg-callbacks-outer.o lbg-callbacks-outer.cc lidia-main.cc: In function ‘int main(int, char**)’: lidia-main.cc:61:18: error: ‘Py_Initialize’ was not declared in this scope lidia-main.cc:62:28: error: ‘PySys_SetArgv’ was not declared in this scope make[1]: *** [lidia-main.o] Error 1 make[1]: *** Waiting for unfinished jobs mv -f .deps/lbg-drag-and-drop.Tpo .deps/lbg-drag-and-drop.Plo mv -f .deps/lbg-callbacks-outer.Tpo .deps/lbg-callbacks-outer.Po mv -f .deps/lbg.Tpo .deps/lbg.Plo make[1]: Leaving directory `/home/ubuntu/autobuild/ubuntu_2013-01-24__T19_00_19/coot-0.7.1-pre/lbg' make: *** [all-recursive] Error 1 make failed. On Thu, Jan 24, 2013 at 6:55 AM, Paul Emsley wrote: > On Thu, 2013-01-24 at 11:35 +, Paul Emsley wrote: > > On Wed, 2013-01-23 at 19:17 -0500, hari jayaram wrote: > > > Hi I am trying to build the subversion coot on a Ubuntu machine > > > running 12.10 using the build-it-gtk2-simple python script. > > > > > > > > > I get all the way to compiling the final coot and get an error in the > > > final linking part. > > > > > > > > > (dynload_shlib.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' > > > /usr/bin/ld: note: 'dlsym@@GLIBC_2.2.5' is defined in > > > DSO > /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu/libdl.so so try > adding it to the linker command line > > > /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu/libdl.so: > > > could not read symbols: Invalid operation > > > collect2: error: ld returned 1 exit status > > > make[1]: *** [coot-real] Error 1 > > > make[1]: Leaving directory > > > > `/home/ubuntu/autobuild/ubuntu_2013-01-23__T22_55_56/coot-0.7.1-pre/src' > > > make: *** [all-recursive] Error 1 > > > make failed. > > > > > > > > > The detailed error is at http://dpaste.com/889587/ > > > > > > > > > I had buidling using a script that Clemens had shared ( which also > > > calls build-it-gtk2-simple) but that too failed at an earlier step. > > > > At a guess I'd suggest putting -ldl after -lpython2.7. That seems a > > sane way of doing things - I don't know why it's not arranged like that > > already. I'll dig... > > > > > $ python-config --ld-flags > -lpthread -ldl -lutil -lm -lpython2.6 > > Urgh! >
[COOT] Building subversion coot on Ubuntu 12.10 64 bit
Hi I am trying to build the subversion coot on a Ubuntu machine running 12.10 using the build-it-gtk2-simple python script. I get all the way to compiling the final coot and get an error in the final linking part. (dynload_shlib.o): undefined reference to symbol 'dlsym@@GLIBC_2.2.5' /usr/bin/ld: note: 'dlsym@@GLIBC_2.2.5' is defined in DSO /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu/libdl.so so try adding it to the linker command line /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu/libdl.so: could not read symbols: Invalid operation collect2: error: ld returned 1 exit status make[1]: *** [coot-real] Error 1 make[1]: Leaving directory `/home/ubuntu/autobuild/ubuntu_2013-01-23__T22_55_56/coot-0.7.1-pre/src' make: *** [all-recursive] Error 1 make failed. The detailed error is at http://dpaste.com/889587/ I had buidling using a script that Clemens had shared ( which also calls build-it-gtk2-simple) but that too failed at an earlier step. Has anyone successfully built coot on 12.10. Thanks a tonne for your help Hari
[COOT] Arrange waters around protein in C2- swap atom with sym-related function?
Hi, I tried Extensions-Modelling-Arrange waters around protein ( my spacegroup is C2) ..but some waters are not re-assigned to what I would consider my parent molecule. I know this is not trivial since these waters are very close to the symmetry axis and it is hard to make the call as to which molecule they should be part of..but one of the symmetry related positions is more useful since it puts the water closer to the active site. Is there a function that swaps a water or any atom with its symmetry mate. Something like "symmetry-swap-water" that I can then click the water and it switches the molecule with its symmetry related one--and deletes the symm related one. Or is there a way to click on a symmetry water and append it to a new object so that I can merge them into the parent molecule. I know I am being lazy..but I wont be surprised if this is lurking somewhere inside coot Thanks Hari
[COOT] libcheck garbled small molecule in ccp4 6.3 but not in ccp4 6.2.2
Hi, I just upgraded to the newest CCP4 version 6.3 and noticed that libcheck which coot uses to produce restraints from a SMILES string produces garbled coordinates in ccp4 version 6.3 , but the same SMILES string works just fine with CCP4 version 6.2. I tried to get it to fail on public molecules , but couldnt find an illustrative example. But consistently the old version 6.2.2 succeeds but 6.3 garbles the phenyl rings. Anyone else seeing this. Thanks Hari
[COOT] svn 4245 coot probe dots dynamically not getting re-drawn post refine
Hello All, I upgraded to svn 4245 on ubuntu 64-Linux 10.04 . I used to have the probe dots get redrawn following a refine prior to this update. ( I was running svn 4222 or something like that). However somehow the coot probe dots are not shown dynamically when picking rotamers, and routine refinement. Here is what I have in my ~/.coot (define *probe-command* "/home/hari/molprobity3/bin/linux/probe") (define *reduce-command* "/home/hari/molprobity3/bin/linux/reduce") (set-do-probe-dots-on-rotamers-and-chis 0) (set-do-probe-dots-post-refine 1) (set-rotamer-lowest-probability 0.5) I am hoping nothing changed on my setup to inactivate the probe dots. Thanks for your help Hari
Re: [COOT] show valence for ligand and add hydrogens to just ligand ? Keep hydrogens during refmac run?
Hi all , Thanks for your replies... In my case Refmac run from inside coot does not preserve hydrogens if present , such as the ones that prodrg puts in .., I will try using modern refmac as Paul recommended... As for the valence ...even if I read in the Cif , the displayed molecule , once it goes through a refmac run from inside coot , defaults back to not showing the double bonds and aromatics. Is there a way to fix that style or make it default. Thanks Hari On Tuesday, April 17, 2012, Ed Pozharski wrote: > On Tue, 2012-04-17 at 11:54 -0400, hari jayaram wrote: > > Currently refmac > > removes the hydrogens during refinement and this may be some > > preference that I toggled and dont remember doing so. > > You mean it removes hydrogens even if you use MAKE HOUT Y? > > -- > Coot verendus est > >
[COOT] show valence for ligand and add hydrogens to just ligand ? Keep hydrogens during refmac run?
Hi , I was wondering how to enable the valence view in coot. Currenty when I prodrg-ify a residue it shows the ligand with aromatic rings and double bonds. Once I run through refmac the view is reset to the usual coot view. Is there a way to have coot show the ligand with double bonds and aromatic rings permanently. Also , Is there a way to add hydrogens to just the ligand ? . Or a setting to have coot keep the hydrogens that prodrg-ify puts into the ligand during a refmac refinement from within coot. Currently refmac removes the hydrogens during refinement and this may be some preference that I toggled and dont remember doing so. I am using the coot 0.7-pre-1 (revision 3748) Thanks Hari
Re: [COOT] [ccp4bb] Ubuntu Maverick and coot menus
Thanks Folmer for the Unity workaround to have my menus stay in one place! http://askubuntu.com/questions/10481/how-do-i-disable-the-global-application-menu As much as I hate Ubuntu Unity ( I agree with most of the opinions expressed here and ccp4bb) I will grin and bear it because of how much easier it has made life with Linux. I will try the workarounds you talked about. Along these lines Gnome3 also seems to have similar issues and then there is OSX Lion...I guess the new usability mantra is have stuff fly all over the place and appear and disappear in graphics card intensive and "intuitive" ways ..such is progress! Hari On Sat, Feb 11, 2012 at 2:58 PM, Folmer Fredslund wrote: > Dear David and everybody, > > lørdag den 11. februar 2012 skrev David Schuller : > >> On 02/11/12 14:15, Nat Echols wrote: >> >> On Sat, Feb 11, 2012 at 10:55 AM, hari jayaram wrote: >> >> There has been a lot of opinions within the Ubuntu community about >> Unity..just wondering what coot-ers are using with the new Ubuntu(s). >> >> ... If this is a >> reliable indication of where Ubuntu is going in the future, I need to >> find a new favorite distribution. >> >> that seems to be a common sentiment: >> >> >> http://www.zdnet.com/blog/hardware/ubuntu-sees-massive-slide-in-popularity-mint-sprints-ahead-but-why/16550 >> >> " >> >> Ubuntu sees massive slide in popularity, Mint sprints ahead..." > > Please note that this is based on pageranks from distrowatch, i.e. this only > shows something about what pages on distrowatch people have been looking at. > It shows absolutely nothing about what people actually use. > > > With respect to the ubuntu UI, I personally am happily using it. > As far as I understand, the "old" gnome UI was abandoned for version 3.0 and > canonical (company behind ubuntu) decided to go somewhere else ( thats the > short description). > > anyways: > You should be able to disable the global application menu as shown here: > http://askubuntu.com/questions/10481/how-do-i-disable-the-global-application-menu > > Best regards > > Folmer > > > >> >> -- >> === >> All Things Serve the Beam >> === >> David J. Schuller >> modern man in a post-modern world >> MacCHESS, Cornell University >> schul...@cornell.edu >> > > -- > Folmer Fredslund > Maj Allé 86 > 2730 Herlev > Mobil: (+45) 61 468 009 > Mail: folm...@gmail.com
[COOT] Ubuntu Maverick and coot menus
This probably belongs on an Ubuntu mailing list ... But I am thinking of switching over to Ubuntu Unity 3d running Maverick meerkat for crystallography. I am currently using gnome2 ( aka gnome old school or just gnome) and Lucid Lynx .. My first observation on a test system with the Unity system are that the coot menus are "OSX-esque and appear and disappear in an annoying manner , undocked from the main coot window and present on the top bar. The menus dont persist ( I do have compiz enabled) 1) Are any users using Coot and Ubuntu Unity desktop ..is there a way to have the menus not appear and disappear in windowed mode 2) are there workarounds that people find work other than falling back to old gnome and staying with Maverick.. 3) Or does the new gnome-shell and Maverick make up for it? There has been a lot of opinions within the Ubuntu community about Unity..just wondering what coot-ers are using with the new Ubuntu(s). Thanks Hari
Re: [COOT] using custom key bindings in wincoot ( where to put .cootrc or equivalent in coot for windows)
Thanks Bernhard, Sorry for not reading your very clear instructions properly. ..My monitor resolution was set crazy high and I missed the dot before the coot.py Once I renamed my key-bindings to dot-coot-dot-py (.coot.py) and placed them into the C:\Wincoot directory..the key bindings work on startup. Thanks again Hari On Thu, Feb 9, 2012 at 3:50 AM, Bernhard Lohkamp wrote: > > Hi Hari, > > the file (in your $HOME) directory should be called .coot.py > (dot-coot-dot-py). The dot in front is important (*)!!! coot.py is a very > different file which is read in somewhere else. > Alternatively put your coot.py file in the directory > $HOME/.coot-preferences/ (again watch out for the dot!, in case the > directory doesnt already exist). > > B > > (*) On Windows there may be the problem to rename it using the explorer. The > DOS shell should allow you to do so. > > >> Hello Bernhard, >> Thanks for your email . >> >> It turns out that my file was not called coot.py and I also had a few >> "hidden" new-line characters due to a copy paste from your wiki python >> key bindings. >> Once I named the file coot.py and corrected the python syntax..I see >> the following behavior: >> >> At startup I do have windows coot inform me that it read in coot.py. >> However the key bindings do not work and do not show up in the User >> key bindings listing. Also activating a shortcut gives a "Key 119is >> not bound message" >> >> If I now read in the same coot.py using the Menu-Run-Script-select >> coot.py. The key-bindings then get registered and show up in the >> listing and work just great. >> >> >> So there is something..maybe in the order the python files are read in >> ..but having a valid coot.py file didnt add the key bindings at >> startup. >> >> I am wondering how I can avoid reading the key bindings in every time >> manually. >> >> Thanks >> Hari >> >> >> On Wed, Feb 8, 2012 at 2:57 AM, Bernhard Lohkamp >> wrote: >>> >>> >>> Hi Hari, >>> >>> python scripts are read in from the following locations (*)(x): >>> >>> - $HOME/.coot.py (equivalent to .coot) >>> - $HOME/.coot-preferences (a directory, all script file from here are >>> read) >>> - $COOT_PYTHON_EXTRAS_DIR (a directory which you can specify yourself) >>> >>> Calculate->Run script should always work. If it doesnt there may be >>> something wrong with the script. What does the DOS console tell you. >>> >>> Hope this helps, >>> >>> B >>> >>> (*) on Windows (currently) $HOME is $COOT_HOME which is the directory >>> WinCoot is installed in >>> >>> (x) wonder if this needs a better documentation, some can be found here: >>> >>> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Startup_files >>> >>> Hi recently found myself using coot on windows and was wondering where the user specific key bindings are to be introduced to coot. This was windows 7 and I think it defines the users home directory as C:\Users\user.name\ , but I know that other Windows versions use "C:\Documents and Settings\user.name" as the home. I tried to add my python coot bindings based off Bernhard Lohkamp to both of those locations and they didnt seem to get picked up. I then tried reading in the script bearing the key bindings using Calculate-Runscript- and picking the filename.py . Strangely that didnt work either. When I then copy-pasted the python script directly into the scripting window within coot using Calculate-Scripting-Python and then pasting in the code there. The key bindings did show up and work proving that there were no in-advertant syntax errors like new line charcaters etc that were corrupting the python syntax in the filename.py. Am I correct in that coot windows only supports python scripting and where do I have my key-bindings python scipt so that they are picked up on startup and show up in Extensions-Settings-Key-bindings. Thanks Hari >>> >>> >>> >>> >>> -- >>> *** >>> >>> Dr. Bernhard Lohkamp >>> Assistant Professor >>> Div. Molecular Structural Biology >>> Dept. of Medical Biochemistry and Biophysics (MBB) >>> Karolinska Institutet >>> S-17177 Stockholm >>> Sweden >>> >>> phone: (+46) 08-52487651 >>> fax: (+46) 08-327626 >>> email: bernhard.lohk...@ki.se > > > > -- > *** > > Dr. Bernhard Lohkamp > Assistant Professor > Div. Molecular Structural Biology > Dept. of Medical Biochemistry and Biophysics (MBB) > Karolinska Institutet > S-17177 Stockholm > Sweden > > phone: (+46) 08-52487651 > fax: (+46) 08-327626 > email: bernhard.lohk...@ki.se
Re: [COOT] using custom key bindings in wincoot ( where to put .cootrc or equivalent in coot for windows)
Hello Bernhard, Thanks for your email . It turns out that my file was not called coot.py and I also had a few "hidden" new-line characters due to a copy paste from your wiki python key bindings. Once I named the file coot.py and corrected the python syntax..I see the following behavior: At startup I do have windows coot inform me that it read in coot.py. However the key bindings do not work and do not show up in the User key bindings listing. Also activating a shortcut gives a "Key 119is not bound message" If I now read in the same coot.py using the Menu-Run-Script-select coot.py. The key-bindings then get registered and show up in the listing and work just great. So there is something..maybe in the order the python files are read in ..but having a valid coot.py file didnt add the key bindings at startup. I am wondering how I can avoid reading the key bindings in every time manually. Thanks Hari On Wed, Feb 8, 2012 at 2:57 AM, Bernhard Lohkamp wrote: > > Hi Hari, > > python scripts are read in from the following locations (*)(x): > > - $HOME/.coot.py (equivalent to .coot) > - $HOME/.coot-preferences (a directory, all script file from here are read) > - $COOT_PYTHON_EXTRAS_DIR (a directory which you can specify yourself) > > Calculate->Run script should always work. If it doesnt there may be > something wrong with the script. What does the DOS console tell you. > > Hope this helps, > > B > > (*) on Windows (currently) $HOME is $COOT_HOME which is the directory > WinCoot is installed in > > (x) wonder if this needs a better documentation, some can be found here: > http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Startup_files > > >> Hi recently found myself using coot on windows and was wondering where >> the user specific key bindings are to be introduced to coot. >> This was windows 7 and I think it defines the users home directory as >> C:\Users\user.name\ , but I know that other Windows versions use >> "C:\Documents and Settings\user.name" as the home. >> I tried to add my python coot bindings based off Bernhard Lohkamp to >> both of those locations and they didnt seem to get picked up. >> >> I then tried reading in the script bearing the key bindings using >> Calculate-Runscript- and picking the filename.py . Strangely that >> didnt work either. >> >> When I then copy-pasted the python script directly into the scripting >> window within coot using Calculate-Scripting-Python and then pasting >> in the code there. The key bindings did show up and work proving that >> there were no in-advertant syntax errors like new line charcaters etc >> that were corrupting the python syntax in the filename.py. >> >> Am I correct in that coot windows only supports python scripting and >> where do I have my key-bindings python scipt so that they are picked >> up on startup and show up in Extensions-Settings-Key-bindings. >> >> Thanks >> >> Hari > > > > -- > *** > > Dr. Bernhard Lohkamp > Assistant Professor > Div. Molecular Structural Biology > Dept. of Medical Biochemistry and Biophysics (MBB) > Karolinska Institutet > S-17177 Stockholm > Sweden > > phone: (+46) 08-52487651 > fax: (+46) 08-327626 > email: bernhard.lohk...@ki.se
[COOT] using custom key bindings in wincoot ( where to put .cootrc or equivalent in coot for windows)
Hi recently found myself using coot on windows and was wondering where the user specific key bindings are to be introduced to coot. This was windows 7 and I think it defines the users home directory as C:\Users\user.name\ , but I know that other Windows versions use "C:\Documents and Settings\user.name" as the home. I tried to add my python coot bindings based off Bernhard Lohkamp to both of those locations and they didnt seem to get picked up. I then tried reading in the script bearing the key bindings using Calculate-Runscript- and picking the filename.py . Strangely that didnt work either. When I then copy-pasted the python script directly into the scripting window within coot using Calculate-Scripting-Python and then pasting in the code there. The key bindings did show up and work proving that there were no in-advertant syntax errors like new line charcaters etc that were corrupting the python syntax in the filename.py. Am I correct in that coot windows only supports python scripting and where do I have my key-bindings python scipt so that they are picked up on startup and show up in Extensions-Settings-Key-bindings. Thanks Hari
[COOT] svn coot 3743 not loading map and pdb after refmac run
Hi, I upgraded and compiled coot from the svn branch after a few months of using an older svn commit id. The new svn 3743 coot with python (build-it-gtk-simple python) on a 64 bit Ubuntu 10.04 box does not seem to load the map and pdb after a refmac run from inside of coot. The previous version ( probably rev around 3600) would run the refmac , popup the xloggraph and also load in the maps and toggle off old maps and toggle on new maps and models ( Very useful feature) Is this particular to my coot build or did something change that I was not aware of. Thanks for your help in advance Hari
Re: [COOT] refmac from within svn 3315 coot not writing pdb and mtz to Current-dir on completion
Sorry for jumping the gun with a question, I found it , and it was rather obvious. Even though I picked current-dir in the coot-refmac dialog. Coot puts the refmac output files into the coot-refmac sub-directory within the current directory. This is new behavior as far as I know. But the project dir is much tidier this way. Thanks Hari On Thu, Jan 20, 2011 at 3:40 PM, hari jayaram wrote: > Hello , > > I am running coot svn revision 3315 on Ubuntu Lucid 10.04 > > When I run refmac5 from within coot with this version of coot , it competes > perfectly and displays the new pdb and the FWT and DELFWT maps from the mtz > file produced by the refmac run. > > On completion coot generally wrote these files ( the pdb and mtz from > refmac) to the current directory or wherever the setting was indicated in > the refmac run coot dialog box. > I generally leave this as current directory > > However I find that with this svn revision these files are not written to > the Current directory. I looked in /tmp and in other places ( find ~/ -name > ...) > But I couldnt find the files. > Of course this is no biggie , I could always explicitly save the pdb, but > the mtz is "lost" as only the maps are loaded. > > Is anyone else seeing this behavior > > Thanks > Hari > > > > > > > > > >
[COOT] refmac from within svn 3315 coot not writing pdb and mtz to Current-dir on completion
Hello , I am running coot svn revision 3315 on Ubuntu Lucid 10.04 When I run refmac5 from within coot with this version of coot , it competes perfectly and displays the new pdb and the FWT and DELFWT maps from the mtz file produced by the refmac run. On completion coot generally wrote these files ( the pdb and mtz from refmac) to the current directory or wherever the setting was indicated in the refmac run coot dialog box. I generally leave this as current directory However I find that with this svn revision these files are not written to the Current directory. I looked in /tmp and in other places ( find ~/ -name ...) But I couldnt find the files. Of course this is no biggie , I could always explicitly save the pdb, but the mtz is "lost" as only the maps are loaded. Is anyone else seeing this behavior Thanks Hari
[COOT] libcheck - SMILES input- knotted ligand models
Hello, I am using the SMILES input based , ligand coordinate and restraint generation inside coot , which I understand calls libcheck. For some of these ligands , the stereochemistry around parts of the molecule are "wrong" : in that the SMILES string has solid bonds instead of wedges. I am using RDKIT the cheminformatics package to visualize these molecules. For these SMILES strings the model generated by libcheck inside coot is very mangled. Such that rings circle around and clash with each other for example. For the present moment I am manually editing the molecule to correct the stereochemistry- generate the SMILES string externally and then have libcheck do the right thing. Is there a way to avoid this second step. I would think that the default model generated my SMILES input inside coot should at-least not have rings forming knots with each other. Also does anyone know if there is a way to flatten SMILES representations -i.e render them devoid of stereochemistry and then have libcheck do the most stable thing. I will crosspost later to ccp4bb in case this is a libcheck problem. Thanks in advance Hari
[COOT] SMILES generated cif and refmac from inside coot
Coot does not seem to be passing its libcheck-SMILES generated cif file to Refmac when the refmac button from inside coot is clicked and refmac is run. IS there someway to have the refmac button be aware of the cif file that is typically in the present working directory. Thanks in advance Hari
[COOT] Ubuntu 10.04 - subversion build gtkglext not configured properly error
Hi I have the habit of using the subversion build of coot and decided to switch to ubuntu 10.04 a few days before it comes out. I am building it using the build-it-gtk2-simple python script The build progresses till the final stage and the "16-coot.txt" indicates checking for pkg-config... (cached) /usr/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. need to update libtool here /home/hari/autobuild/hari_2010-04-14__T13_58_50/coot-0.6.2-pre-1 make: *** No targets specified and no makefile found. Stop. make failed. I am seeing the gtkglext-1.0 pc in the apropriate directories in the build h...@hari:~/coot-read-only$ find ~/* -name "gtkglext-1.0.pc" /home/hari/autobuild/hari_2010-04-14__T13_36_31/gtkglext-1.2.0/gtkglext-1.0.pc /home/hari/autobuild/coot-pre-release-gtk2-python/lib/pkgconfig/gtkglext-1.0.pc But still get that error. The other log files dont seem to have anything wrong. Any ideas on how to get past this hurdle. Thanks Hari
[COOT] refmac from inside coot and NCS checkbox
Hello everyone, I know that coot reads in the pdb file and figures out the ncs relationships upon loading . When you run refmac from inside coot and click the button, I am assuming it uses the computed NCS relationships as restraints during refinement . My pdb file does have the NCS definitions in the header , but I was not sure if coot was using those if I checked the box. Also, in pdb file I have four bound chloride ions to my four protein chains A,B,C,D . The new chlorides were assigned to 4 new chains E,F.G,H when I added them , for some reason refmac run from inside coot seems to have issues with that and stopped with some error . I am sorry I didnt note down the error , But assigning those Cl atoms to their respective chains a la the new pdb style got refmac from inside coot to chug right along and refine the model.. Thanks for your help and comments Hari
[COOT] coot distributed by ccp4-6.1.3 and python scripting
Hi, I noticed that the coot distributed by ccp4-6.1.3 does not have python built into it. Is there anyway to add in the python support post installation ? I am running the ccp4 supplied coot on OSX Leopard 10.5.8 I am cc-ing the coot mailing list as well . Thanks Hari
[COOT] nan sigma when I try to make Dano map in expert mode
Hi , I am seeing this problem only on a particular 32 bit machine. On this machine when I try to make a map using a Dano column and PHIC or PHIDM , coot chugs through the calculation. Creates the map object in Display manager and then no map shows up. Despite any extent of attempting to scroll the map the sigma gets reported as "nan". All dialogs alkso have the map sigma as "nan" I know there is nothing wrong with the mtz file as the same file works on all other machines running coot regardless of version number . The fft from mtz does not have any problems making FWT maps , only Dano maps give this strange behavior. Any ideas how to fix this Thanks for your help Hari The command it hiccups on is (make-and-draw-map-with-reso-with-refmac-params "/home/yilingf/Desktop/cootbuild/cootbuild/caded-hg2ph-80_dmmulti3-32_4.mtz" "/unknownrenamed/unknown100409:11:15:15/DANO_Se32-4" "/HKL_base/HKL_base/PHI_madsad" "" 0 0 1 "/unknown/unknown100409:04:37:39/F_hg2" "" "/HKL_base/HKL_base/FreeR_flag" 1 1 0 -1.00 -1.00) ^Cmaking conventional map from MTZ filename /home/yilingf/Desktop/cootbuild/cootbuild/caded-hg2ph-80_dmmulti3-32_4.mtz using /unknownrenamed/unknown100409:11:15:15/DANO_Se32-4 /HKL_base/HKL_base/PHI_madsad CCP4MTZfile: Mtz column type mismatch: DANO_Se32-4 D-F Number of OBSERVED reflections: 53182 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 84, 108, 162) INFO:: 0.262 seconds to read MTZ file INFO:: 0.027 seconds to initialize map INFO:: 12.616 seconds for FFT INFO:: 1.389 seconds for statistics Map mean: nan Map sigma: ... nan Map maximum: . -1e+10 Map minimum: . 1e+10 INFO:: 0.059 seconds for contour map INFO:: 14.353 seconds in total INFO:: Stored refmac parameters: /unknown/unknown100409:04:37:39/F_hg2 /HKL_base/HKL_base/FreeR_flag is sensible. (make-and-draw-map-with-reso-with-refmac-params "/home/yilingf/Desktop/cootbuild/cootbuild/caded-hg2ph-80_dmmulti3-32_4.mtz" "/unknownrenamed/unknown100409:11:15:15/DANO_Se32-4" "/HKL_base/HKL_base/PHI_madsad" "" 0 0 1 "/unknown/unknown100409:04:37:39/F_hg2" "" "/HKL_base/HKL_base/FreeR_flag" 1 1 0 -1.00 -1.00) (graphics-molecule-bond-type 2)
Re: [COOT] Add rotation function to "add terminal residue" command
I agree with Donald, and would add my vote to a possible feature request for coot. It would be great if the added residue could also be rotated and translated concurrently with addition . That way you could position the atoms where you think they should go in one step. This will really help chain extension and loop filling for the low resolution areas . Hari On Wed, Jul 1, 2009 at 8:49 AM, Donald Damian Raymond wrote: > Hi Stefan, > Thanks a lot for the hint, but that gives me even less control over where I > place my new residues. I guess for now I will just have to place new > residues in the correct density in two steps. > -Donald > > > Stefan Gerhardt wrote: > >> >> Or you add in your .coot file the following… >> >> (set-terminal-residue-do-rigid-body-refine 0) >> >> (set-add-terminal-residue-do-post-refine 1) >> >> (set-mutate-auto-fit-do-post-refine 1) >> >> Cheers >> >> Stefan >> >>
Re: [COOT] [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...
Hi I am wondering if there is a linux nvidia driver update or any other hack that allows Crystal Eyes 3 stereo products to work with the LCD 120Hz flat panel monitors. I should have read Warrens warning post (Dated Jan 23 , 2009 [ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet) , before purchasing the Viewsonic VX2265wm 120Hz LCD. But my CRT died last week and since I was addicted to pymol/coot-in stereo ( with Crystal Eyes 3 ) , I rushed out and bought this 120 Hz LCD monitor. Of course things dont work . And I am wondering if there is any update from nvidia or any other workaround that allows me to get stereo on this setup. Monitor : Viewsonic FuHzion VX2265wm 120Hz Graphics card: Quadro FX 4600 OS: Ubuntu Linux X86_64 - Hardy Heron 8.04 Stereo glasses: Crystal Eyes 3 with 3pin mini din connector Thanks for your help in advance Hari Jayaram Brandeis University On Tue, Feb 10, 2009 at 1:54 PM, Warren DeLano wrote: > > Donnie, > > This tripped me up for a while too, but I think the stereo DIN is an > output (for projector, & Z-screens, etc.) not an input. Suffice it to > say that the nVidia USB dongle does not work (in my hands, with or > without USB power) as a VESA-based emitter the way we apparently both > hoped it would! > > Cheers, > Warren > > > -Original Message- > > From: Donnie Berkholz [mailto:dberkh...@gentoo.org] > > Sent: Tuesday, February 10, 2009 9:49 AM > > To: Warren DeLano > > Cc: pymol-us...@lists.sourceforge.net > > Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet... > > > > On 23:26 Thu 22 Jan , Warren DeLano wrote: > > > I tested out the Samsung Syncmaster 2233RZ / NVIDIA 3D Vision bundle > > > today ($599 for a 120 Hz LCD display with one pair of glasses). > > > > > I was very much hoping that this new display would nevertheless also > > > work with existing nVidia Quadro-based Mac or Linux systems with > > > existing emitters and glasses running existing OpenGL software. > Sadly, > > > this does not seem to be the case due at least in part to the fact > that > > > the phase of the sync signal coming out of the Quadro card does not > > > match the update phase of the LCD display. In addition, light from > the > > > display itself seems to corrupt the sync signal for StereoGraphics > > > glasses. > > > > Hi Warren, > > > > Did you happen to try the new glasses + emitter with a CRT? I am > > particularly curious whether this works on Linux, or whether it needs > > some sort of USB driver stubs so that Linux knows what to do with > these > > devices. > > > > It comes with a stereo-DIN cable so it seems like it could work, > > provided the emitter can get power via USB and the glasses can charge > > via USB. > > > > If the new glasses can work with a CRT, then at least we could buy > > stereo bundles now and use all of the parts of them in some sort of > > Frankenstein setup pending support for LCD stereo. > > > > -- > > Thanks, > > Donnie > > > > Donnie Berkholz > > Developer, Gentoo Linux > > Blog: http://dberkholz.wordpress.com > > > > -- > Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) > software. With Adobe AIR, Ajax developers can use existing skills and code to > build responsive, highly engaging applications that combine the power of local > resources and data with the reach of the web. Download the Adobe AIR SDK and > Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com > ___ > PyMOL-users mailing list > pymol-us...@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[COOT] quick shortcut or script to zero occupancy using mouse
Hi I have a very low resolution map in which I can barely see side chains . I want to set to zero occupancy many residues and residue side-chains before I do a refinement. Currently I am using the Residue-Info menu item to set each occupancy to zero residue by residue . And in cases where part of the residue is seen , atom-by-atom inside this menu entry. Is there a mode where I can keep the mouse active and clicking an atom will set the occupancy to zero - and I can embark on a clickfest setting atoms to zero occupancy. Thanks for your help Hari
[COOT] Ubuntu Jaunty (9.04) subversion build works great now
Hello Paul and everyone, Since I had complained about difficulties in building coot from subersion on Ubuntu Jaunty , I thought I should write in to say that I tried building the subversion revision 2021 on ubuntu 9.04 from scratch and it builds just fine and everything works great However the "build-it-gtk2-simple python" build script seems to always build into two directories the : $AUTOBUILD_BUILD/coot-pre-release-gtk2-python AND $AUTOBUILD_BUILD/coot-Linux-i686-ubuntu-9.04-gtk2-python For my 32 bit 9.04 running ubuntu the coot-pre-release-gtk2-python/bin/coot binary works just fine . The coot-Linux-i686-ubuntu-9.04-gtk2-python/bin/coot stops with a message (GThread-ERROR **: GThread system may only be initialized once.). Is that because it may be a 64 bit build? So I am guessing I have to give some command line switch to the script to suppress the i686 build on this ubuntu 32bit 9.04 box. Regardless I am happily cooting with the latest build on Jaunty jackalope. Thanks a tonne Hari On Tue, May 12, 2009 at 11:11 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 > method<http://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 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] subversion build on ubuntu 9.04 fails : [: =: unary operator expected error
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 method<http://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 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. >
[COOT] subversion build on ubuntu 9.04 fails : [: =: unary operator expected error
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 Just thought I would write in , in case anybody was seeing the same problem or has a solution SOme of the other stuff also spooled to screen before the failure to build is pasted below: Thanks for your help Hari --2009-05-08 16:14:52-- http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/guile/guile-1.8.5.tar.gz Resolving www.mirrorservice.org... 212.219.56.133, 212.219.56.134, 212.219.56.138, ... Connecting to www.mirrorservice.org|212.219.56.133|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3933369 (3.8M) [application/x-gzip] Server file no newer than local file `/home/hari/autobuild//sources/guile-1.8.5.tar.gz' -- not retrieving. ./build-it-gtk2-simple: line 2395: 127: command not found --2009-05-08 16:16:05-- http://www.ysbl.york.ac.uk/~emsley/software/extras/net-http-0.3.1.tar.gz Resolving www.ysbl.york.ac.uk... 144.32.72.243 Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 26907 (26K) [application/x-gzip] Server file no newer than local file `/home/hari/autobuild//sources/net-http-0.3.1.tar.gz' -- not retrieving. configure: warning: cannot execute guile-config configure: warning: cannot execute NONE-guile-config configure: warning: cannot execute NONE-guile-config ./configure: 580: is: not found sed: can't read Makefile: No such file or directory make: *** No rule to make target `install'. Stop. --2009-05-08 16:16:08-- http://www.ysbl.york.ac.uk/~emsley/software/extras/greg-2.0.0-pe.tar.gz Resolving www.ysbl.york.ac.uk... 144.32.72.243 Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 453770 (443K) [application/x-gzip] Server file no newer than local file `/home/hari/autobuild//sources/greg-2.0.0-pe.tar.gz' -- not retrieving. --2009-05-08 16:16:17-- http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/guile-gtk/guile-gtk-2.1.tar.gz Resolving www.mirrorservice.org... 212.219.56.138, 212.219.56.139, 212.219.56.153, ... Connecting to www.mirrorservice.org|212.219.56.138|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 781985 (764K) [application/x-gzip] Server file no newer than local file `/home/hari/autobuild//sources/guile-gtk-2.1.tar.gz' -- not retrieving. --2009-05-08 16:16:23-- http://www.ysbl.york.ac.uk/~emsley/software/extras/guile-gui-0.2.tar.gz Resolving www.ysbl.york.ac.uk... 144.32.72.243 Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 33885 (33K) [application/x-gzip] Server file no newer than local file `/home/hari/autobuild//sources/guile-gui-0.2.tar.gz' -- not retrieving. --2009-05-08 16:16:24-- http://www.ysbl.york.ac.uk/~emsley/software/extras/neil-jerram.guile-gui.patch Resolving www.ysbl.york.ac.uk... 144.32.72.243 Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3779 (3.7K) [text/plain] Server file no newer than local file `/home/hari/autobuild//sources/neil-jerram.guile-gui.patch' -- not retrieving. --2009-05-08 16:16:24-- http://www.ysbl.york.ac.uk/~emsley/software/extras/guile-gui-patch-post-neil.patch Resolving www.ysbl.york.ac.uk... 144.32.72.243 Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3799 (3.7K) [text/plain] Server file no newer than local file `/home/hari/autobuild//sources/guile-gui-patch-post-neil.patch' -- not retrieving. --2009-05-08 16:16:25-- http://download.gna.org/guile-lib/guile-lib-0.1.6.tar.gz Resolving download.gna.org... 78.40.121.79 Connecting to download.gna.org|78.40.121.79|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 508682 (497K) [application/x-tar] Server file no newer than local file `/home/hari/autobuild//sources/guile-lib-0.1.6.tar.gz' -- not retrieving. BUILDING coot: version coot-0.6-pre-1-revision-1994, python=yes --2009-05-08 16:16:27-- http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.6-pre-1-revision-1994.tar.gz Resolving www.ysbl.york.ac.uk... 144.32.72.243 Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 10851590 (10M) [application/x-gz
Re: [COOT] svn revision 1950 and rigid body fit zone
Hi paul, Kevin did write to me asking if I could submit a detailed bug report. Strangely, I could not reproduce the problem. I am still running revision 1950 ..On that day myself and one other person ( I think it was Dr Eleanor Dodson) reported that the rigid body fit zone ..was stopping after the first click. I have since used rigid body fit zone many times without any problem in rev 1950 I had two more unrelated issues. # Add terminal residue and simultaneous movement Didnt coot previously also allow you to simultaneously rotate-translate a terminal atom concurrently with the addition. Now in revision 1947 onwards. Clicking add terminal residue only allows you to move the atom around using the mouse . So all end residue additions are two steps , first add, then accept and then again rotate translate zone to position. Is this intended. # Copy_from_ncs_master_to_others : creates all atoms as stars in ncs mates Thanks hari On Thu, Apr 23, 2009 at 4:34 PM, Paul Emsley wrote: > hari jayaram wrote: > >> Hello , >> >> I just noticed that rigid body fit zone in revision 1950 stops expecting >> user mouse clicks after clicking on the first atom . >> >> Is anyone else seeing this. >> >> >> > Hi Hari, > > Do you mean rigid body fit or Rotate/Translate mode? (Rotate/Translate can > go into "single click mode" (it's designed to)). > > I can't reproduce the problem of rigid body fit going into "single click > mode" > > Paul. >
[COOT] svn revision 1950 and rigid body fit zone
Hello , I just noticed that rigid body fit zone in revision 1950 stops expecting user mouse clicks after clicking on the first atom . Is anyone else seeing this. Also the Extensions-All Molecule MR stepped refine crashes at random points after going through about 200-400 residues ( I noticed this with rev 1947 and updated..but am seeing it with revision 1950 as well) I am running Ubuntu Hardy Heron ( 8.04 , 64 bit , coot subversion gtk2 python build ) Thanks Hari
Re: [COOT] coot -lsq to output transformation matrix like ssm?
Please ignore my previous message: Coot lsq does spit out the matrix. I was confused because in the cases where it cannot find the equivalent residues . And so it fails to find a transformation operator , coot still generates a copy of the moving molecule . This made me think that the transformation had worked even though the stdout clearly indicated it had not Hari On Sun, Apr 12, 2009 at 3:42 AM, hari jayaram wrote: > Hi I am using the latest build (1947 0.6 pre) of coot > > Coot lsq superpose does exactly what I want it to do i.e superpose all the > atoms from one set of fragments to the ncs symmety other set of fragments. > > Is it possible to have coot output to stdout the transfomation matrix like > it does when it does a ssm match. > > SSM superpose fails on this case since the superposed entities are still > poly-ALA . I have tried getting lsqkab from ccp4 to behave and do the same > thing but its quite tedious to teach lsqkab which chains are related. > > I know coot-lsq does the right thing , Is it possible for it to spit out > the transformation matrix for lsq as well . > > Thanks > hari > >
[COOT] coot -lsq to output transformation matrix like ssm?
Hi I am using the latest build (1947 0.6 pre) of coot Coot lsq superpose does exactly what I want it to do i.e superpose all the atoms from one set of fragments to the ncs symmety other set of fragments. Is it possible to have coot output to stdout the transfomation matrix like it does when it does a ssm match. SSM superpose fails on this case since the superposed entities are still poly-ALA . I have tried getting lsqkab from ccp4 to behave and do the same thing but its quite tedious to teach lsqkab which chains are related. I know coot-lsq does the right thing , Is it possible for it to spit out the transformation matrix for lsq as well . Thanks hari
[COOT] problem with subversion build using build-it-gtk2-simple since 1859
Hello ,I was getting used to building the latest and bleeding edge coot every few days using the subversion build script build-it-gtk2-simple. ( as per instructions in ttp:// strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code_via_autobuild_scripts ) However since revision 1859 , the build script stops a few seconds after downloading the newest source and then signals "coot build failed ". I am seeing the newest source *.gz fully downloaded but nothing happens after that. Sadly the buildnotes and build.log file do not have any indication of the problem. My system is a Ubuntu 64 bit hardy heron 8.04 and the builds were always successful till 1859 . Since I am missing living on the edge . Can anyone help me troubleshoot the unexplained build failure. Thanks in advance Hari Jayaram
Re: [COOT] pymol does not cartoon-ize my "helices" : coot helical restraints
DSSP did indeed think they were helices. Also thanks for the sec str coloring tip-didnt realize coot had that feature. For the model coot also colors the helices pink as would be expected. So it must be that pymol cartoons still dont implement "DSSP" ..which I thought was the case Hari On Sat, Feb 7, 2009 at 8:24 AM, Paul Emsley wrote: > hari jayaram wrote: > >> I have a low-ish resolution (3.5 ) map for a membrane protein. I have been >> using helical restraints heavily in pymol to do the model building (versions >> 0.4.2 to 0.5.1 to 0.6 pre release ) . The structure is very homologous to >> something else and these are really long membrane spanning helices. So a >> large part of the structure should be helical and thats my justification >> for using the restraints in coot. >> >> I have mostly refined in refmac ( newest 5.3 ) and some in phenix. Both of >> these pick the refining restraints automagically. >> >> My problem is that my helices look perfect in coot , with the torsions and >> h-bonding looking pretty good .All the traffic lights ( with and without >> torsional and ramchandran and helical restraints) are green. But pymol >> simply refuses to cartoonize my "helices" as helix. >> >> I know I can force the pymol cartoon algorithm to treat those regions as >> helix but am concerned that something is not correct in the way I built my >> model. >> >> Any clues on forcing my helices to conform to what pymols idea of a helix >> is. The pymol version is also 1.0r2 and does cartoonize everything else as >> expected. >> > > Are the residues in helical secondary structure? (the DSSP algorithm is > built in to Coot - perhaps Pymol uses something else to define ss?) > > You can look at the sequence view (coloured by secondary structure) or view > as CA with Secondary Structure to see if Coot (at least) thinks your > residues are alpha helices. > > Paul. >
[COOT] pymol does not cartoon-ize my "helices" : coot helical restraints
I have a low-ish resolution (3.5 ) map for a membrane protein. I have been using helical restraints heavily in pymol to do the model building (versions 0.4.2 to 0.5.1 to 0.6 pre release ) . The structure is very homologous to something else and these are really long membrane spanning helices. So a large part of the structure should be helical and thats my justification for using the restraints in coot. I have mostly refined in refmac ( newest 5.3 ) and some in phenix. Both of these pick the refining restraints automagically. My problem is that my helices look perfect in coot , with the torsions and h-bonding looking pretty good .All the traffic lights ( with and without torsional and ramchandran and helical restraints) are green. But pymol simply refuses to cartoonize my "helices" as helix. I know I can force the pymol cartoon algorithm to treat those regions as helix but am concerned that something is not correct in the way I built my model. Any clues on forcing my helices to conform to what pymols idea of a helix is. The pymol version is also 1.0r2 and does cartoonize everything else as expected. Hari Jayaram
[COOT] coot crashes on delete-zone?
Hi everyone, I was trying to delete a range of residues in my molecule using the delete zone option. The last commands echoed to console during the run were set-delete-residue-zone-mode followed by clear-pending-delete-item Coot did delete the region and then beachballed and stayed frozen before it updated the centre and moved the map over. I have had this bring coot , X and my machine down twice and thought I would write in. The particulars of the installation are: coot binary: 0.5-pre1 revision 958 python gtk2 , binary from W.G Scott X quartz version 2.2.0.1 installed two days back after W.G Scotts email Platform: Mac Pro running OSX Leopard 10.5.2 Thanks Hari On Mon, Apr 28, 2008 at 4:44 AM, Kevin Cowtan <[EMAIL PROTECTED]> wrote: > Don't use clipper from my site - you've probably picked up the new > threaded version - we haven't tested this with coot yet. > > You should run Paul's build-it-gtk2-simple script, which should build all > the dependencies for you. > http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple<http://www.ysbl.york.ac.uk/%7Eemsley/build-logs/build-it-gtk2-simple> > > > hari jayaram wrote: > > > Hi , Bill, > > Sorry I skipped this mail and have not yet tried the rpm you send out > > for 0.4.1 on my redhat machine. ( see below) > > > > I really feel the need to get the traffic-lights working and get coot > > 0.5-pre-1 compiled on my gentoo linux machine. > > I have been trying to do get the compile to work > > > > The coot configure command fails to see my clipper libraries. I have > > built my clipper libraries from scratch using the shell script on Kevin > > Cowtans page < > > http://www.ysbl.york.ac.uk/%7Ecowtan/clipper/doc/p_installation.html>. > > The clipper build completed successfully and got installed in > > /usr/local/clipper > > > > For coot, The configure command I am using is > > > > " ./configure --with-python=/usr/lib/python2.5 --with-glib-prefix=/usr > > --with-glut-prefix=/usr/lib --with-gtk-prefix=/usr > > --with-gtkgl-prefix=/usr/lib/gtkglext-1.0 --with-gtkgl-prefix=/usr > > --with-clipper-prefix=/usr/local/clipper > > --with-mmdb-prefix=/usr/local/clipper/lib > > --with-ssmlib-prefix=/usr/local/clipper/lib/" > > > > > > Coot still refuses to "see" the library. ALso, just once , the > > configure command did get past the Clipper library check and was running a > > "cc1plus" command. That command continued running for around 2 hrs and I > > finally killed the process. Now the configure gives the same output ..i.e > > > > "checking for gsl-config... /usr/local/bin/gsl-config > > checking for GSL - version >= 1.3... yes > > checking for glib-config... /usr/bin/glib-config > > checking for GLIB - version >= 1.2.8. <http://1.2.8.>.. yes > > checking for gtk-config... /usr/bin/gtk-config > > checking for GTK - version >= 0.99.7. <http://0.99.7.>.. yes > > checking for GL... yes > > checking for GtkGLArea... yes > > checking for GtkCanvas... yes > > checking for GLUT... yes > > checking for MMDB... yes > > checking for SSMLib... /usr/local/clipper/lib/ > > checking for Clipper... no > > Error locating Clipper - a shiny new version of Clipper is required now > > " > > Any help in getting a brand new version of coot with traffic lights > > compiled will be greatly appreciated > > Thank you for all your help > > Hari > > > > > > > > On Wed, Apr 16, 2008 at 7:18 PM, William Scott < > > [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote: > > > >Please see if this works: > > > > > > http://diablo.ucsc.edu/~wgscott/debian/rpm/coot-0.4.1-1.i386.rpm<http://diablo.ucsc.edu/%7Ewgscott/debian/rpm/coot-0.4.1-1.i386.rpm> > ><http://diablo.ucsc.edu/%7Ewgscott/debian/rpm/coot-0.4.1-1.i386.rpm> > > > >If it does, I'll put together a 0.5-pre1 version. > > > > > > > >On Apr 16, 2008, at 2:09 PM, Paul Emsley wrote: > > > >hari jayaram wrote: > > > >Hi I noticed that there is no redhat gtk2 version of coot > >0.5pre 1 rev 958 or even earlier > >I guess that means I am going to have to compile coot on my > >redhat machine to get access to the traffic-lights and other > >features > > > >Can I cast my vote for a redhat python-gtk2 binary > > > > > >I tried quite hard to do this (on RH8). > > > >I failed and gave up. > > > >Paul. > > > > > > > > >
Re: [COOT] gtk2 version for redhat
Hi , Bill, Sorry I skipped this mail and have not yet tried the rpm you send out for 0.4.1 on my redhat machine. ( see below) I really feel the need to get the traffic-lights working and get coot 0.5-pre-1 compiled on my gentoo linux machine. I have been trying to do get the compile to work The coot configure command fails to see my clipper libraries. I have built my clipper libraries from scratch using the shell script on Kevin Cowtans page <http://www.ysbl.york.ac.uk/%7Ecowtan/clipper/doc/p_installation.html>. The clipper build completed successfully and got installed in /usr/local/clipper For coot, The configure command I am using is " ./configure --with-python=/usr/lib/python2.5 --with-glib-prefix=/usr --with-glut-prefix=/usr/lib --with-gtk-prefix=/usr --with-gtkgl-prefix=/usr/lib/gtkglext-1.0 --with-gtkgl-prefix=/usr --with-clipper-prefix=/usr/local/clipper --with-mmdb-prefix=/usr/local/clipper/lib --with-ssmlib-prefix=/usr/local/clipper/lib/" Coot still refuses to "see" the library. ALso, just once , the configure command did get past the Clipper library check and was running a "cc1plus" command. That command continued running for around 2 hrs and I finally killed the process. Now the configure gives the same output ..i.e "checking for gsl-config... /usr/local/bin/gsl-config checking for GSL - version >= 1.3... yes checking for glib-config... /usr/bin/glib-config checking for GLIB - version >= 1.2.8... yes checking for gtk-config... /usr/bin/gtk-config checking for GTK - version >= 0.99.7... yes checking for GL... yes checking for GtkGLArea... yes checking for GtkCanvas... yes checking for GLUT... yes checking for MMDB... yes checking for SSMLib... /usr/local/clipper/lib/ checking for Clipper... no Error locating Clipper - a shiny new version of Clipper is required now " Any help in getting a brand new version of coot with traffic lights compiled will be greatly appreciated Thank you for all your help Hari On Wed, Apr 16, 2008 at 7:18 PM, William Scott <[EMAIL PROTECTED]> wrote: > Please see if this works: > > http://diablo.ucsc.edu/~wgscott/debian/rpm/coot-0.4.1-1.i386.rpm<http://diablo.ucsc.edu/%7Ewgscott/debian/rpm/coot-0.4.1-1.i386.rpm> > > If it does, I'll put together a 0.5-pre1 version. > > > > On Apr 16, 2008, at 2:09 PM, Paul Emsley wrote: > > hari jayaram wrote: >> >>> Hi I noticed that there is no redhat gtk2 version of coot 0.5pre 1 rev >>> 958 or even earlier >>> I guess that means I am going to have to compile coot on my redhat >>> machine to get access to the traffic-lights and other features >>> >>> Can I cast my vote for a redhat python-gtk2 binary >>> >> >> I tried quite hard to do this (on RH8). >> >> I failed and gave up. >> >> Paul. >> > >
[COOT] gtk2 version for redhat
Hi I noticed that there is no redhat gtk2 version of coot 0.5pre 1 rev 958 or even earlier I guess that means I am going to have to compile coot on my redhat machine to get access to the traffic-lights and other features Can I cast my vote for a redhat python-gtk2 binary Thanks Hari
Re: [COOT] real space refinement and regularize at 3.3 A- no traffic lights
Hi Paul.. Thanks for that detailed reply.. I am quite convinced that It was just my paranoia that had me seeing regularize-zone try to fit in with density. But , I am curious as to why you would never use regularize-zone. At my lowish resolution I really have been using it to make sure my geometry stays acceptable.Maybe I should just leave regions with bad density un-modelled. As for the traffic-lights I cannot see it with the version I got from the coot nighties. I thought the coot script links to all dependencies statically and it seems to be calling libraries that came with the download. So I assume it should be linking to gtk 1.2 , but I am not not seeing the traffic lights or the permament model-refine sidebar on my redhat Linux box. I did see it on the fink installed coot 0.5 pre 1 on OSX however. I will tinker around trying to get the traffic light to show up.. Thanks for your help Hari On Tue, Apr 15, 2008 at 4:18 PM, Meyer, Peter <[EMAIL PROTECTED]> wrote: > > > >3) Also I just noticed that I can adjust my weights for the real space > >refine zone to favor my geometry more than my map. Any idea what are > >reasonable weights for a 3.3 A map with very few side chains and no > >carbonyl bumps visible. I find that real space refine does quite often > tend > >to swing my side chains into neighboring mainchain density even though it > is > >obviously wrong. Is there a way to reduce this behavior or avoid it. > > I've had decent luck using the same weight as I give refmac (although this > is with coot 0.3.3; coot seems to have jumped version numbers while I wasn't > looking). > > Pete >
[COOT] real space refinement and regularize at 3.3 A
Hi I am using coot 0.5 pre 1 on linux . I am trying to correct the model after molecular replacement into a 3.3 A map and I have a few questions The map is quite good for all the helical regions but the loops are expectedly hard to build. Thanks to prime-and-witch I have a remarkably bias removed map that I am building into with coot. 1) I am noticing that Regularize-zone seems quite "aggressive" in this version of coot compared to the version I was used to (coot 0.3). In addition , if I understand correctly regularize should not care whether the region being regularized is in or out of density. Is that true? . It seems that sometimes regularize seems to really go out of its way to make it into density..or it may just be my model! 2) It seems that even though some of my model came from "good" geometry for a 2.5 A data derived model, regularize seems to modify it extensively . Is this to be expected. 3) Also I just noticed that I can adjust my weights for the real space refine zone to favor my geometry more than my map. Any idea what are reasonable weights for a 3.3 A map with very few side chains and no carbonyl bumps visible. I find that real space refine does quite often tend to swing my side chains into neighboring mainchain density even though it is obviously wrong. Is there a way to reduce this behavior or avoid it. 4) I had one final question, I used 0.5 pre 1 on Mac osx a few days back and could have sworn that a real space refinement also pulls up an on-the-fly graph of the "goodness" of bond angles, lengths etc every time the command is run . The three bar graphs were color coded from green to red. Is that no longer available in linux 0.5 pre 1 or do I have to turn that option on somewhere. Your help and comments will be greatly appreciated Hari
[COOT] Segmentation fault on OSX coot when I try to calculate NCS maps
Hi everyoneI have a rather low-resolution map 3.5 A with a lot of NCS i.etwo copies of a dimer . I was looking into doing some non-crystallographic averaging in coot However when I run the NCS maps GUI menu item . Coot proceeds through the calculation and promptly crashes. The stdout messages are not very helpful. I am using a fink installed binary and coot version 0.5-pre-1 mango:~ hari$ coot --version 0.5-pre-1 (revision 852) [with guile 1.8.3 embedded] [with python 2.5.1embedded] find_ncs_matrix returns | -0.5886,0.8078,-0.032| |0.8048,0.5893, 0.07076| | 0.07602,0.0159,-0.997| (-105.1, 51.13,-12.43) INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A INFO:: max_xmaps :0 INFO:: xmap_list :0x1c59184 INFO:: installing xmap_list :0x28f2804 Segmentation fault wondering if I can get this to work before I resort to lsqkab or rave to get my NCS maps. Though neither of them are as easy to use as Coot Hari
Re: [COOT] Is there anything I can do to make X11 stable enough to use on 10.5.2
We just got our brand new leopard running mac pro , we have been having frequent crashes and freeze ups as well Leopard version : 10.5.2 X version: 2.1.4 Coot version:0.5.1 Intel Mac Pro Most downright crashes where I had to resort to the power button came when i was runing coot. When running ccp4i , it seems understandably less taxing on X. But even with that I always have the gui windows bleed through into other windows. Not to mention the fact that spaces is entirely unuseable. To think that linux has had outstanding "spaces" like multiple desktop functionality for years.. Just my rant against leopard and X and I agree with Bills sentiment..makes me want to go back to gentoo-linuxbut then we just spent almost 3K on this machine and I am sure hoping these problems will soon disappear A willing guinea pig Hari Jayaram On Sun, Mar 23, 2008 at 6:19 AM, Phil Evans <[EMAIL PROTECTED]> wrote: > Bill > > I've been using 10.5.2 plus the X11 2.1.4 update from the Xquartz > site, & I haven't had problems with freezing lately, I _think_ not > since this update. The main problem is that Exposé doesn't work properly > > not much help ... > > Phil > > (looking at a white Easter outside the bedroom window) > > On 23 Mar 2008, at 01:01, William Scott wrote: > > > Hi Folks: > > > > I know I've asked before, but it is so frustrating to lose an hour > > of work, trying to convince myself that I won't get reamed this > > time. But I keep going back, like to some sort of abusive > > codependent relationship, to put it into California terms. > > > > I'm using a molecular graphics model building crystallography > > program called coot, but this happens with enough other X11 > > applications that I don't think it is the fault of coot. Prior to > > OS X 10.5, I never ever had a problem with X11. > > > > If I try to resize a window while the program is loading, it is a > > guarantee that the Xserver will freeze. However, if I try to be > > real careful, I can start to get work done, but then when some > > window or pop-up menu appears, a half hour or an hour into a session > > of work, I'll get a random freeze. > > > > I'm running 10.5.2 on intel (but this happens on all my 10.5.2 > > computers, ppc and intel) and the latest X11 from the update page, > > and when I sample the frozen processes I get this as output: > > > > > > > > > > > > > > > > My kids want to know why I swear at the computer so much. I'm almost > > ready to reformat the disk and install ubuntu linux. > > > > Thanks. > > > > Bill Scott > > > > > > > > >
Re: [COOT] mouse focus issues in 0.5-pre-1 (revision 852) despite com.apple.x11 wm_ffm true
Thanks William Scott, defaults write org.x.X11 wm_ffm -bool true Worked very well. I of course had to restart X to get it to get X to update this parameter. I now had mouse focus back in Leoaprd 10.5.2 with the graphics update ( Xquartz 2.1.4) Maybe I should put this into the wiki/FAQ. I was just noticing that the rotamer analysis still flags a lot of the rotamers as being bad. I didnt realize I was using version 0.2 on our old lab machine. I did read that after 0.4 , coot switched to using David Richardsons library. Is it possible to use the old library. Are the large number of flagged rotamers still a known issue? Thanks for your help and sorry to add to this thread with a unrelated question Hari Jayaram Brandeis University On Thu, Mar 20, 2008 at 12:45 PM, William Scott <[EMAIL PROTECTED]> wrote: > They keep changing the name of the damn plist file. > > Try > > org.x.X11 > > same for all the other defaults commands, like stereo (anyone get it > working with coot on 10.5 yet?) > > > William G. Scott > > Contact info: > http://chemistry.ucsc.edu/~wgscott/<http://chemistry.ucsc.edu/%7Ewgscott/> > > > On Mar 20, 2008, at 8:58 AM, hari jayaram wrote: > > > $ defaults write com.apple.x11 wm_ffm true > >
[COOT] mouse focus issues in 0.5-pre-1 (revision 852) despite com.apple.x11 wm_ffm true
Hi everyone.. We just bought a new mac pro in the lab. I installed coot on this machine. And this time remembered to set the X11 mouse focus using $ defaults write com.apple.x11 wm_ffm true However this does not seem to do the trick and I find I need to double click everytime I select an option in the external GUI as well as to select a residue for a real space refine etc. Clicking on the gui thats on the right hand side of main coot window however enables me to do everything with just a "normal" single click. I did restart X and coot and set the defaults with and without sudo , but the focus is still messed up. The machine is a multiuser machine running OSX 10.5.2 and X quartx 2.1.4 and coot version 0.5-pre-1 (revision 852) [with guile 1.8.3 embedded] [with python 2.5.1embedded] This does seem to be an OS issue , but does anybody know how this can be corrected. IS there something in a multi-user setup that I need to do differently Thanks a lot for your help in advance Hari Jayaram Brandeis University
Re: [COOT] refmac bug in 0.4.1?
Hi everyone Thanks for helping me fix the "double click" or mouse focus issues on MAC OSX.. As Paul emailed a simple trick fixed my mouse focus issues $ defaults write com.apple.x11 wm_ffm true I however cannot get the refmac command to run from inisde this coot version 0.4.1 ( revision 647) The error is the same as reported by W.G Scott. in a previous email . I am of course giving it my F , SIGF .but it seems to not know where my pdb file is.. (safe_scheme_command) Error in proc: key: wrong-number-of-args args: (#f Wrong number of arguments to ~A ( etc etc My OS version :OSX 10.5.2 X11 version : 2.1 Any ideas on how to get around this ( other than running refmac separately of course) Thanks for your help Hari Jayaram On Tue, Jan 22, 2008 at 1:52 AM, William Scott <[EMAIL PROTECTED]> wrote: > Hi Paul et al: > > I am currently using coot 0.4.1 that I compiled. > > If I load in a pdb file and its corresponding mtz file, I can use > refmac to calculate its map, and this works. > > If I then try to use the "run refmac" command in the model/fit/refine > menu, I am rewarded with the following error: > > > Running refmac refmac params molecule number 4 > DEBUG:: pdb_in_filename is now 1 coot-refmac > DEBUG:: pdb_in_filename is now 2 coot-refmac/ > DEBUG:: pdb_in_filename is now 3 coot-refmac/mpr006_refine_004_refmac0- > pre.pdb > DEBUG:: mtz_out_filename: coot-refmac/mpr006_refine_004_refmac0.mtz > DEBUG:: pdb_out_filename: coot-refmac/mpr006_refine_004_refmac0.pdb > refmac ccp4i project dir > (run-refmac-by-filename "coot-refmac/mpr006_refine_004_refmac0- > pre.pdb" "coot-refmac/mpr006_refine_004_refmac0.pdb" "coot-refmac/ > refmac-for-phases.mtz" "coot-refmac/mpr006_refine_004_refmac0.mtz" "" > 0 0 4 1 0 '' -1 "" "/mpr08006_1/Unspecified/F_08006" "/mpr08006_1/ > Unspecified/SIGIMEAN") > ((safe_scheme_command) Error in proc: key: wrong-number-of-args > args: (#f Wrong number of arguments to ~A (# filename (pdb-in-filename pdb-out-filename mtz-in-filename mtz-out- > filename extra-cif-lib-filename imol-refmac-count swap-map-colours- > post-refmac? imol-mtz-molecule show-diff-map-flag phase-combine-flag > phib-fom-pair force-n-cycles ccp4i-project-dir f-col sig-f-col . r- > free-col)>) #f)) > > > Anyone else getting this (apart from my postdoc)? > > Thanks in advance. > > Bill >
Re: [COOT] Coot 0.4.1 rev 647 on 10.5.2 + Graphics Driver Update
Hi I am sorry to bother this group with a trivial question..my googling skills did not yield an answer. I am running coot on OS X 10.5.2 with X11 2.1.1 and its been a while since I have refined a structure ( last time I did so was with coot on linux a year ago) This is my first time running coot on OSX or a mac . But why is it that I have to double click to select a residue or a residue range and double click to select a button in the Model/fit/refine menu curtain. All my mac apps and X11 apps like ccp4i etc seem to respond fine to button clicks like "normal" i.e single click to toggle etc. But coot seems to require double click when the cross haris change for picking a residue range ( like for the real space refine option). I am wondering ig I can change this behavior I am using the fink binary from W.G Scott Thanks Hari On Wed, Feb 13, 2008 at 12:33 AM, William Scott <[EMAIL PROTECTED]> wrote: > Someone told me about the following trick to unfreeze X11 on OS X: > > If it freezes, try starting the "Activity Monitor" program and then click > on the X11 process and then "Sample Process". This can sometimes unfreeze > it, and you can continue with coot or whatever program. > > Juergen Bosch wrote: > > Yes, I'm running X11 2.1.1 > > > > Before the update to 10.5.2 it worked fine for me as far as I can tell. > > > > Jürgen > > > > William Scott wrote: > > > >>I was getting weird behavior with the latest X11, but the 10.5.2 update > >>actually downgraded it to 2.1.1, which seems more stable. Is that what > >>you have now? > >> > >>Juergen Bosch wrote: > >> > >> > >>>Hi all, > >>> > >>>I updated yesterday to 10.5.2 and then also installed the Graphics > >>>Driver Update, since then I get funny behaviour of Coot in combination > >>>with X11, namely it freezes on me sometimes sometimes not and it always > >>>has something to do with changing window size or opening a new dialog > >>>field. When I then force kill X11 and restart Coot I get a GTK error > >>>message. > >>> > >>>Anybody out there sharing the same experience ? I actually recompiled > >>>Coot via Fink with my current system but that didn't help much. > >>> > >>>Thanks for any suggestions, > >>> > >>>Jürgen > >>> > >>>-- > >>>Jürgen Bosch > >>>University of Washington > >>>Dept. of Biochemistry, K-426 > >>>1705 NE Pacific Street > >>>Seattle, WA 98195 > >>>Box 357742 > >>>Phone:+1-206-616-4510 > >>>FAX: +1-206-685-7002 > >>>Web: http://faculty.washington.edu/jbosch > >>> > >>> > >>> > >> > >> > >> > > > > > > -- > > Jürgen Bosch > > University of Washington > > Dept. of Biochemistry, K-426 > > 1705 NE Pacific Street > > Seattle, WA 98195 > > Box 357742 > > Phone: +1-206-616-4510 > > FAX: +1-206-685-7002 > > Web: http://faculty.washington.edu/jbosch > > > > > > >
