[ccp4bb] Install coot in linux
Since I can't access http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ I installed coot by installing ccp4. However, I can't launch coot in my terminal (I logged in with ssh -X) with a below message. Since it mentions something about Gtk, I tried to install gtk3, but http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple is not accessible (https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Installation_from_a_distributed_binary_tarball_package). Additionally, direct installation of gtk3 seems not trivial with many dependencies that need sudo right. Is there anyone contact info of emsley? Thank you (base) [kimd999@kriosgpu bin]$ ./coot (coot-bin:79769): GLib-GObject-WARNING **: g_object_set_valist: object class 'GtkSettings' has no property named 'gtk-application-prefer-dark-theme' INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /opt/apps/ccp4-7.1/lib/data/monomers/ There are 166 data in /opt/apps/ccp4-7.1/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/a/ALA.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/a/ASP.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/a/ASN.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/c/CYS.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/g/GLN.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/g/GLY.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/g/GLU.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/p/PHE.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/h/HIS.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/i/ILE.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/l/LYS.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/l/LEU.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/m/MET.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/m/MSE.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/p/PRO.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/a/ARG.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/s/SER.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/t/THR.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/v/VAL.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/t/TRP.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/t/TYR.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/p/PO4.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/s/SO4.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/g/GOL.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/c/CIT.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/e/EDO.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/a/A.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/c/C.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/g/G.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/u/U.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/d/DA.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/d/DC.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/d/DG.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/d/DT.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/h/HOH.cif There are 2 data in /opt/apps/ccp4-7.1/lib/data/monomers/n/NA.cif INFO:: Reading coordinate file: /opt/apps/ccp4-7.1/share/coot/standard-residues.pdb INFO:: file /opt/apps/ccp4-7.1/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 The program 'coot-bin' received an X Window System error. This probably reflects a bug in the program. The error was 'BadValue (integer parameter out of range for operation)'. (Details: serial 311 error_code 2 request_code 149 minor_code 3) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) 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 permi
Re: [ccp4bb] Install coot in linux
On 21/10/2020 17:40, Doo Nam Kim wrote: Since I can't access http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ That link was extant 2004-2007. I installed coot by installing ccp4. OK - watch out for 0.9.1 though - it's the chicken's elbows! However, I can't launch coot in my terminal (I logged in with ssh -X) with a below message. Since it mentions something about Gtk, I tried to install gtk3, Wow - good for you! Gtk3 is Future Coot (Gtk4 is Future Future Coot). (FWIW, you can build and install Future Coot - by which I mean, there's a script to do so - who knows if it will work, of course) but http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple is not accessible (https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Installation_from_a_distributed_binary_tarball_package). Yeah. :-( that is the sad fate of URLs. In my opinion if one publishes a URL it should be available for the next 50 years - or until the end of humanity (whichever happens sooner)). Not all web server administrators share this point of view. Additionally, direct installation of gtk3 seems not trivial with many dependencies that need sudo right. That is correct in every respect. Is there anyone contact info of emsley? Well... the Home of Coot is a peripatetic entity, whose current location is https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ There is a Coot mailing list available via Jiscmail: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=COOT These may be more useful than Emsley himself. If you wish you can find his contact details by searching for them on the MRC LMB site. The program 'coot-bin' received an X Window System error. This probably reflects a bug in the program. The error was 'BadValue (integer parameter out of range for operation)'. (Details: serial 311 error_code 2 request_code 149 minor_code 3) OpenGL over GLX was never a full club member. Coot (well, at least *that* Coot) was designed to run locally and if it ever ran remotely then it seems that you had crossed the appropriate palm with the requisite amount of silver. Hope that helps, Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] [Resolved] Re: [xds] how to specify measuring angle
Dear all, What I knew is starting angle (-60) and ending angle (+60). Additionally, I know number of image files generated by mrc2smv is 120 from my mrc files. Since it is conventional to delete/omit first/last image, changing into a decently "accurate" approximation as STARTING_ANGLE=-60 DATA_RANGE=2 119 OSCILLATION_RANGE=1 reproduced my predecessor's completeness. Thank you all To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [Resolved] Re: [xds] how to specify measuring angle
Hello, I am interested to know why "it is conventional to delete/omit first/last image". Forgive my ignorance. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Original Message On 21 Oct 2020, 19:23, Doo Nam Kim wrote: > Dear all, > > What I knew is starting angle (-60) and ending angle (+60). > Additionally, I know number of image files generated by mrc2smv is 120 from > my mrc files. > > Since it is conventional to delete/omit first/last image, > > changing into a decently "accurate" approximation as > > STARTING_ANGLE=-60 > DATA_RANGE=2 119 > OSCILLATION_RANGE=1 > > reproduced my predecessor's completeness. > > Thank you all > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [Resolved] Re: [xds] how to specify measuring angle
Hi Jon, The goniometer on a TEM microscope typically cannot rotate the full 360 degrees and therefore we can't ramp it up to speed before initiating collection and slow it down after collection has ended as is typically done for X-ray crystallography. This causes the tilt speed and therefore the oscillation per frame to be less reliable in the early and late frames. We added a small delay between starting the stage tilt and exposing the crystal/collecting the first image to help with this. Best regards, Jessica On Wed, Oct 21, 2020 at 2:30 PM Jon Cooper < 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > Hello, I am interested to know why "it is conventional to delete/omit > first/last image". Forgive my ignorance. > > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com > > > > > > Original Message > On 21 Oct 2020, 19:23, Doo Nam Kim < > 4e720d49e642-dmarc-requ...@jiscmail.ac.uk> wrote: > > > Dear all, > > What I knew is starting angle (-60) and ending angle (+60). > Additionally, I know number of image files generated by mrc2smv is 120 > from my mrc files. > > Since it is conventional to delete/omit first/last image, > > changing into a decently "accurate" approximation as > > STARTING_ANGLE=-60 > DATA_RANGE=2 119 > OSCILLATION_RANGE=1 > > reproduced my predecessor's completeness. > > Thank you all > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > -- Jessica Bruhn, Ph.D Principal Scientist NanoImaging Services, Inc. 4940 Carroll Canyon Road, Suite 115 San Diego, CA 92121 Phone #: (888) 675-8261 www.nanoimagingservices.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
