[COOT] Unable to refine ligand in coot
I am trying to refine a protein with two ligands. One of the ligands apparently will not allow me to do real space refinement in coot after I import it as a cif file, created from sketcher. It is a known ligand in structure deposited in the pdb as 1RQI. I could not retrieve the ligand with the three letter code and the file looks similar to the other ligand, except it contains a sulfur. Any help would be appreciated. Bobby Barnett
Re: [COOT] Release 0.7
Additional Linux builds are in RPM repositories linked here: http://software.opensuse.org/download?project=home:wojdyr:ccp4&package=coot For now only packages for Fedora16, 17 and OpenSuse 12.1 are visible, but a few others, including CentOS 6, are being built now and will be available soon. All are configured without guile-gtk, and OpenSuse without guile at all. If anything else is missing, let me know. The packages hasn't been tested much, so use at own risk. Marcin On 29 September 2012 18:30, William G. Scott wrote: > Additional OS X builds are linked here: > > http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot > > > > On Sep 29, 2012, at 2:49 AM, Paul Emsley wrote: > >> Mac 10.8: >> >> http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/Coot-0.7-stable_64bit_10.8.2.pkg.zip >>
Re: [COOT] Unable to refine ligand in Coot
Hi Bobby, > I am trying to refine a protein with two ligands. One of the > ligands apparently will not allow me to do real space refinement in > coot after I import it as a cif file, created from sketcher. It is not clear to me what reason you have for using sketcher (it is not the first tool that jumps to (my) mind to use with ligands these days). > It is a known ligand in structure deposited in the pdb as 1RQI. I see DST, IPR and DPO. The restraints for each of those are autoloaded using the standard refmac monomer library (I am using CCP4 6.3, but I would imagine that the same would happen using 6.2). Just "click click" on an atom of the residue and refinement starts. > I could not retrieve the ligand with the three letter code and the > file looks similar to the other ligand, Hmm... oh dear (if by "retieve" you mean what I would call "auto-load"). > except it contains a sulfur. I am not sure what TLCs you mean.Is coot giving you an error message? If so, what is it? Regards, Paul.
Re: [COOT] Release 0.7
Last but not least, the Windows version: http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-download.html Bernhard P.S. Blame Python and Bill Gates for the delay ;-) Hi Coot-users, We are pleased to announce Release 0.7 of Coot. Source: http://lmb.bioch.ox.ac.uk/coot/software/source/releases/coot-0.7.tar.gz Binaries: http://lmb.bioch.ox.ac.uk/coot/software/binaries/releases/ Mac 10.8: http://psbmini.ucsc.edu/~wgscott/coot/stablereleases/Coot-0.7-stable_64bit_10.8.2.pkg.zip Now stick a fork in me (as they say)... Paul. A few notes: o FEATURE: RCrane [RNA builder] o FEATURE: Cootaneer [RNA builder] o FEATURE: Het-groups are now represented with bond orders. o FEATURE: Ligand Builder - working in conjunction with cprodrg. o FEATURE: JLigand interface. o CHANGE: symmetry operator number are no longer zero indexed. Add trans component to symmetry file names. o CHANGE: Dotted surfaces now are coloured by atom type and are at atomic radii rather than 1A. o CHANGE: map transformation no longer has symmetry overwrite problems. -- *** 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
