Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Choosing one of the desired program/instance windows and pressing F10 is probably the most simple way. F10 will show you all windows open accosiated with the one you choose. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 31, 2012, at 10:13 AM, Miguel Ortiz Lombardía wrote: Le 30/10/12 20:28, Jason Busby a écrit : Another work-around is to use the command-tilde (⌘ + ~) keystroke. That will cycle through all the windows of the current program. Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 31/10/2012, at 4:58 AM, Damian Niegowski wrote: If you choose to use the excellent Mac OSX feature Exposé and Active screen corners this becomes less of a problem. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 30, 2012, at 4:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike Hi, I don't know for your osx version (mine is 10.6.8) but the short-cut I know is command-grave accent (⌘ + `). One problem with this is that osx considers all X11-based applications to be a single X11 application, so it can take a while until you reach the window you want if you have other X11-based applications open. Another problem is that, contrary to what you have in aqua-based applications, the X11 windows don't cycle. Apple developers have known about these issues for a long, long time. Perhaps they solved them in more recent versions of osx. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université 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 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
On OSX 10.6.8.(Show Leopard) which was the system in question this option exist, but you are right, the key used might be different. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 31, 2012, at 10:38 AM, Antony Oliver wrote: Unfortunately, that very much depends on which OSX you are running (Leopard, Snow Leopard, Lion, Mountain Lion) and which keyboard you have…! On my keyboard it's F3 and not F10. T. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Oct 31, 2012, at 9:30 AM, Damian Niegowski wrote: Choosing one of the desired program/instance windows and pressing F10 is probably the most simple way. F10 will show you all windows open accosiated with the one you choose. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 31, 2012, at 10:13 AM, Miguel Ortiz Lombardía wrote: Le 30/10/12 20:28, Jason Busby a écrit : Another work-around is to use the command-tilde (⌘ + ~) keystroke. That will cycle through all the windows of the current program. Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 31/10/2012, at 4:58 AM, Damian Niegowski wrote: If you choose to use the excellent Mac OSX feature Exposé and Active screen corners this becomes less of a problem. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 30, 2012, at 4:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike Hi, I don't know for your osx version (mine is 10.6.8) but the short-cut I know is command-grave accent (⌘ + `). One problem with this is that osx considers all X11-based applications to be a single X11 application, so it can take a while until you reach the window you want if you have other X11-based applications open. Another problem is that, contrary to what you have in aqua-based applications, the X11 windows don't cycle. Apple developers have known about these issues for a long, long time. Perhaps they solved them in more recent versions of osx. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université 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 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
If you choose to use the excellent Mac OSX feature Exposé and Active screen corners this becomes less of a problem. Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39 On Oct 30, 2012, at 4:32 PM, Eike Schulz wrote: Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike
[ccp4bb] refinement of ligands
Dear all, I am currently trying to refine co-crystallized ligand structures at 2.8-3.4 Å resolution. After initial molecular replacement the density in the maps, both 2Fo-Fc and Fo-Fc looks good and the ligand seams to have bound. However after running Refmac directly on the output files the maps get much worse. I am using a clean pdb, without ligand or water for the Phaser and subsequent Refmac runs. Also when refining with the ligand in the B factors are a lot higher for the ligand then the surrounding residues, only when lowering the occupancy to 0.7-0.8 for the ligand the B factors look better. Is that acceptable to do at this resolution? R-free is in the 0.24-0.27 range. There is only a marginal change in R-free with the addition of ligand. TLS refinement seams to help alot for overall R values but does not improve the maps. I have also tried Phenix with simulated annealing, rigid body and reference structures. So the question is how best to proceed with refinement at the rather low resolution?? Regards, Damian Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39
