[COOT] how to do sphere refinement
Good evening everybody, I wanted to try sphere refinement for the real space refinement of a glycosidic bond, however it did not work out... (Coot 0.6-pre-1/Durham (revision 2264)) That's what I did: I copied this script into a text file: (add-key-binding Refine residues in a sphere R (lambda () (let ((active-atom (active-residue))) (if (list? active-atom) (let* ((centred-residue (list-head (cdr active-atom) 3)) (imol (car active-atom)) (other-residues (residues-near-residue imol centred-residue 3.5)) (all-residues (if (list? other-residues) (cons centred-residue other-residues) (list centred-residue (refine-residues imol all-residues)) and then loaded into coot by using run script. Then I centered on an atom of my glycan and pressed shift-r, or opened the key bindings under extensions/settings and used the button for my new key binding. Nothing happened, but I got this error message in the terminal, where I started coot: (graphics-general-key-press-hook 82) 82 not found in key_bindings (graphics-general-key-press-hook 114) 114 not found in ((82 R Refine residues in a sphere #procedure #f ())) 114 not found in key_bindings What did I miss or do wrong? Thanks for you help! Sara
Re: [COOT] how to do sphere refinement
Hi Sara, I have the python version in my ~/.coot.py file: ---cut--- def key_binding_func_1(): from types import ListType active_atom = active_residue() if (not active_atom): add_status_bar_text(No active residue) else: imol = active_atom[0] chain_id = active_atom[1] res_no= active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] centred_residue = active_atom[1:4] other_residues = residues_near_residue(imol, centred_residue, 5) all_residues = [centred_residue] if (type(other_residues) is ListType): all_residues += other_residues print imol: %s residues: %s %(imol, all_residues) refine_residues(imol, all_residues) add_key_binding(Refine residues in a sphere, R, lambda: key_binding_func_1()) ---cut--- In principle, if you place your scheme script in your ~/.coot file it will work next time you open coot (without having to load the script). Having said that, it would be great if sphere refinement would take into account atoms on residues from symmetry-related molecules (perhaps it does already so? I tried a few weeks/months ago...) HTH, Miguel Le 8 janv. 2010 à 17:22, Sara Züger a écrit : Good evening everybody, I wanted to try sphere refinement for the real space refinement of a glycosidic bond, however it did not work out... (Coot 0.6-pre-1/Durham (revision 2264)) That's what I did: I copied this script into a text file: (add-key-binding Refine residues in a sphere R (lambda () (let ((active-atom (active-residue))) (if (list? active-atom) (let* ((centred-residue (list-head (cdr active-atom) 3)) (imol (car active-atom)) (other-residues (residues-near-residue imol centred-residue 3.5)) (all-residues (if (list? other-residues) (cons centred-residue other-residues) (list centred-residue (refine-residues imol all-residues)) and then loaded into coot by using run script. Then I centered on an atom of my glycan and pressed shift-r, or opened the key bindings under extensions/settings and used the button for my new key binding. Nothing happened, but I got this error message in the terminal, where I started coot: (graphics-general-key-press-hook 82) 82 not found in key_bindings (graphics-general-key-press-hook 114) 114 not found in ((82 R Refine residues in a sphere #procedure #f ())) 114 not found in key_bindings What did I miss or do wrong? Thanks for you help! Sara -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 smime.p7s Description: S/MIME cryptographic signature
Re: [COOT] coot 0.6.1-pre update - osx 10.6 - problem with mtz and map files
Are you using the 32-bit or 64-bit coot? I have to confess only having checked the 64-bit version (which worked ok in my hands). On Jan 7, 2010, at 9:31 PM, Jan Abendroth wrote: Hi all, I am trying to update coot on osx 10.6 from a 0.6-pre version to the current fink version (0.6.1-pre). Doing the usual fink spiel (fink selfupdate, fink index ...) I ran into some issues during 'fink update-all': a few packages that are dbus and dbus-dependent would not install. All the rest of the core packages could be installed manually. Coot now would install just fine (fink install coot) after I removed the old installation (fink remove coot). Now coot starts up fine as 0.6.1, coordinates can be read, analyzed and modified. However, I cannot read in maps from mtz files, see message from the xterminal below. Coot actually totally freezes in this process. Similarly, ccp4 maps cannot be read in either due to a issue with space groups. Any ideas would be highly welcome Jan reading in mtz file ... initalize graphics molecules...done. (handle-read-draw-molecule-with-recentre 204964c6_2009-10-26_als503_i213_xds_refmac21-coot-Ab31.pdb 1) Reading coordinate file: 204964c6_2009-10-26_als503_i213_xds_refmac21-coot-Ab31.pdb PDB file 204964c6_2009-10-26_als503_i213_xds_refmac21-coot-Ab31.pdb has been read. Spacegroup: I 21 3 Cell: 135.38 135.38 135.38 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 170/172 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: NCS found from matching Chain B onto Chain A Molecule 0 read successfully coot-real(86853,0xa01cd500) malloc: *** error for object 0x2650a00: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug [... same message many times over ...] Spacegroup_registry: ASU warning, LGhash=0x Spacegroup_registry: ASU fail INFO:: not an mtz file: 204964c6_2009-10-26_als503_i213_xds_refmac21.mtz reading in a ccp4 style map: saved directory name: /Users/jan/deCODE/ssgcid/AnphA.01382.a/ccp4/ CCP4 map filename: /Users/jan/deCODE/ssgcid/AnphA.01382.a/ccp4/204964c6_2009-10-26_als503_i213_xds_refmac21_2Fofc.map INFO:: map file type was determined to be CCP4 type allocating space in read_ccp4_map attempting to read CCP4 map: /Users/jan/deCODE/ssgcid/AnphA.01382.a/ccp4/204964c6_2009-10-26_als503_i213_xds_refmac21_2Fofc.map Spgr_cacheobj: symops fail -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
