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=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=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 with error. >> > >> > I'll try to move forward
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=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] 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 bernhard.lohk...@ki.sewrote:
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)
[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
[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
[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 pems...@mrc-lmb.cam.ac.ukwrote: 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] 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] 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 bernhard.lohk...@ki.se 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 Lohkampbernhard.lohk...@ki.se 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 bernhard.lohk...@ki.se 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
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 hari...@gmail.com 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] 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] [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 war...@delsci.com 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 hari...@gmail.com wrote: Hello , The jaunty 32 bit build seems to fail ( with subversion revision 2002 as well) It seems like based on what Ed Pozharsky wrote in ..its a problem with guile in Ubuntu jaunty (9.04) .. On my 32 bit , 9.04 installation , the build-it-gtk2-simple script chugs along fine and then declares the following contradictory message checking for Clipper... yes Congratulations, you are using Guile checking for guile... no configure: error: guile required but not found Regardless ..I will try Bill Scots or the CCP4 wiki methodhttp://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Custom_building_Coot_from_source_codeof separately compiling all the coot dependencies . But though I would wrote in to inquire if there was already a simpler fix. Thanks Hari On Fri, May 8, 2009 at 7:35 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote: 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 methodhttp://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Custom_building_Coot_from_source_codeof separately compiling all the coot dependencies . But though I would wrote in to inquire if there was already a simpler fix. Thanks Hari On Fri, May 8, 2009 at 7:35 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote: 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)
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 paul.ems...@bioch.ox.ac.ukwrote: 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] 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] 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-simplehttp://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.rpmhttp://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.
[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
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: Sample of X11.txt x11_hosing.txt 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
[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] 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
