Re: [COOT] SGI dials and coot?
You're probably better off getting a Powermate. The thing doesn't come close to dials in terms of convenience but it works smoothly with O, coot and PyMOL. Andreas On Mon, Jan 11, 2010 at 4:47 AM, Oliver Clarke cla...@wehi.edu.au wrote: Hi all, Apologies if this has been asked before - does anyone know if it is possible (and if so, how) to get an SGI dial box to work with Coot 0.6? Cheers, Oliver Clarke On 10/01/2010, at 11:01 AM, COOT automatic digest system wrote: From: COOT automatic digest system lists...@jiscmail.ac.uk Date: 10 January 2010 11:01:12 AM To: COOT@JISCMAIL.AC.UK Subject: COOT Digest - 8 Jan 2010 to 9 Jan 2010 (#2010-6) Reply-To: Mailing list for users of COOT Crystallographic Software COOT@JISCMAIL.AC.UK There is 1 message totalling 62 lines in this issue. Topics of the day: 1. OS X /fink coot update problems From: William G. Scott wgsc...@chemistry.ucsc.edu Date: 10 January 2010 7:11:02 AM Subject: OS X /fink coot update problems Yo: Several people wrote to me in the last couple of days about different problems with respect to the latest coot update in fink. This all happened at the beginning of term so I haven't really had enough time to deal with this systematically. Briefly, I put coot 0.6 is in the stable and unstable branch of fink sometime around the Unorthodox Holiday. Subsequently I updated two dependency packages in the unstable branch of fink: guile18-gtk and clipper, and then updated to one of the 0.6.1 pre-releases in unstable (revision-2678). I don't want to touch what is in stable until I know it is in fact stable. Any or all of these could have created problems (although I tested these on a variety of machines and didn't notice anything). If you run the command % fink list -i coot clipper guile18-gtk you should see something like this: Information about 8154 packages read in 1 seconds. i clipper-shlibs 1:2.1-14 Object-oriented crystallographic libraries i coot 0.6.1-pre-1-1 Crystallographic molecular graphics i coot-shlibs 0.6.1-pre-1-1 Crystallographic molecular graphics i guile18-gtk 2.1-2 Glue code to link gtk to guile i guile18-gtk-shlibs 2.1-2 Glue code to link gtk to guile If you have earlier versions, please update. I also recommend (a) having the most recent version of Xcode (the apple compilers, etc) compatible with your OS (b) Apple's official X11 distribution if you are on 10.6 or plan to update to 10.6. (c) if you have a 64-bit capable machine, use the 64-bit fink, ccp4, etc. as this is the future If I haven't gotten back to you, email me again please, and include every relevant detail (version of OS X, fink version, Xcode version, X11 version, output of above command, etc.) and I will do my best to try to deduce what might be problematic. Meanwhile, please accept my apologies. Bill __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __
Re: [COOT] SGI dials and coot?
On Jan 11, 2010, at 4:38 AM, Andreas Förster wrote: Every time I'd ask a question You really ought to update. 0.1 is a bit long in the beak.
[COOT] AW: [COOT] how to do sphere refinement
Thanks Miguel, but is there another way to do this sphere refinement? I'm working on a shared computer and have no administrator rights and also no experience with python/file handling of coot. Or else, if there is no other way, can somebody explain me exactly what I have to do/type (like copying a coot.py file into a local folder and change that, but how then to tell coot to use this file?) Thanks a lot! Sara -Ursprüngliche Nachricht- Von: Mailing list for users of COOT Crystallographic Software [mailto:c...@jiscmail.ac.uk] Im Auftrag von Miguel Ortiz Lombardia Gesendet: Freitag, 8. Januar 2010 18:17 An: COOT@JISCMAIL.AC.UK Betreff: 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
Re: [COOT] how to do sphere refinement
2010/1/11 Sara Züger szue...@bioc.uzh.ch Thanks Miguel, but is there another way to do this sphere refinement? I'm working on a shared computer and have no administrator rights and also no experience with python/file handling of coot. Or else, if there is no other way, can somebody explain me exactly what I have to do/type (like copying a coot.py file into a local folder and change that, but how then to tell coot to use this file?) Coot will automatically use ~/.coot.py if present - all you need to do is copy-and-paste Miguel's code snippet. You don't need administrator rights, since you're only modifying your home directory. -Nat
Re: [COOT] SGI dials and coot?
Hi All, I'm not opposed to integrating this into the latest version of coot, as long as I can get a commitment from the Coot maintainers (Hi Paul :), that we can get it into the main branch. The only other caveat is that I don't have access to an adapter that is known to work with the SGI dials on an Intel based Mac. So if someone can send me a model/part number I can get one ordered. I'm not on this mailing list, so please be sure to cc me if you need my input on something. Regards, Dave On Jan 11, 2010, at 9:11 AM, William G. Scott wrote: David Gohara wrote this. My guess is he could be talked into getting it working. He is exceptionally helpful and extremely knowledgeable, so in my humble opinion he would be a perfect contributor. On Jan 11, 2010, at 4:38 AM, Andreas Förster wrote: Paul, I can imagine building MacDials from a USB hub and eight PowerMates. Would even be cheaper than the original dials, and glow blue. But everyone has old dials lying around... The SBGrid implementation of the dials worked beautifully. It would be so nice to have that available in the current release of coot because 0.1 doesn't really cut it anymore, does it? Every time I'd ask a question on the mailing list, you'd be entirely justified to admonish me to upgrade to the latest coot. Andreas On 11/01/2010 12:09, Paul Emsley wrote: Oliver Clarke wrote: Apologies if this has been asked before - does anyone know if it is possible (and if so, how) to get an SGI dial box to work with Coot 0.6? Yes and no. The SBGrid build a version of Coot-0.1 with sgi dials enabled for Mac OS X (it may still be available on their web site). (They gave me the interface code, but I was never able to compile it, so it didn't make it into the main line.) As Andreas says, a PowerMate is the way to go for now, if you have a Mac. You can bind various rotations to generate key presses and configure Coot to react to key presses. I believe that you can plug in several PowerMates and use them together (not tried it myself though). Paul. -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [COOT] AW: [COOT] how to do sphere refinement
Hi Sara, As Nat said, you just need to create a file in your home area called .coot.py (the dot before 'coot.py' is important) where you simply paste the python code. Use 'vi', 'emacs', 'nedit' or whatever text editor you like. That may be different if you use ms-windows? Others can say... BTW, to put the record straight: it is not 'my' code but Bernhard's. I took it from: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Bernhards_key_bindings_for_coot.py You may need administrative privileges is to have a coot binary with python scripting enabled. But maybe your binary is already python-enabled and you need to do anything but creating your .coot.py file. Or you can install coot in your home area. Best, Miguel Le 11 janv. 2010 à 18:36, Sara Züger a écrit : Thanks Miguel, but is there another way to do this sphere refinement? I'm working on a shared computer and have no administrator rights and also no experience with python/file handling of coot. Or else, if there is no other way, can somebody explain me exactly what I have to do/type (like copying a coot.py file into a local folder and change that, but how then to tell coot to use this file?) Thanks a lot! Sara -Ursprüngliche Nachricht- Von: Mailing list for users of COOT Crystallographic Software [mailto:c...@jiscmail.ac.uk] Im Auftrag von Miguel Ortiz Lombardia Gesendet: Freitag, 8. Januar 2010 18:17 An: COOT@JISCMAIL.AC.UK Betreff: 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 -- 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
