[PyMOL] default settings
Hi All, PyMol has it's own default settings, many of them are the historically accepted ways to view structures, universally accepted colors, etc. and that is great, because when someone uses the program they have to start with something! :) And I realize most users probably open a pdb, work on, close the program, and then don't use it again for days or weeks. However, once someone uses the program all day long, day after day after day, once someone moves beyond the basics, develops a unique color set, develops a new style, develops a better style, or is working on a project that requires dozens, or even hundreds of renderings that all need to based on defaults that are different from the original defaults the program has built in, it gets to be quite a pain to have to run a default script every time one loads another pdb to a working open window, or when one opens another running window of PyMol. Is there anyway to change the default settings in PyMol so that when I open the program, it is using my specified defaults? or perhaps there is a way a script can automatically be run at startup? Or automatically run when I fetch in a new pdb? I'm running MacPyMol on 10.8. Thanks H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] cross hair for non-bonded atoms
Hi, Just wondering how to remove the cross hair that is shown for each non-bonded atom (for example water molecules). Thanks, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr - -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] default settings
On Wed, Jan 30, 2013 at 8:33 AM, H. Adam Steinberg a...@steinbergs.us wrote: Is there anyway to change the default settings in PyMol so that when I open the program, it is using my specified defaults? or perhaps there is a way a script can automatically be run at startup? Or automatically run when I fetch in a new pdb? I'm running MacPyMol on 10.8. Yes, just create a file ~/.pymolrc and add whatever settings you want - for instance, this is mine: set auto_zoom = 0 set cartoon_oval_length = 0.8 set cartoon_oval_width = 0.15 set cartoon_rect_length = 0.8 set cartoon_rect_width = 0.15 set ray_shadows = 0 set ray_opaque_background = 0 -Nat -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] cross hair for non-bonded atoms
Hi Pascal, hide nonbonded Cheers, Jason Sent from my Android. Please excuse the concision and any typos. On Jan 30, 2013 1:10 PM, Pascal Auffinger p.auffin...@ibmc-cnrs.unistra.fr wrote: Hi, Just wondering how to remove the cross hair that is shown for each non-bonded atom (for example water molecules). Thanks, Pascal - Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffin...@ibmc-cnrs.unistra.fr - -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] default settings
This is great, but looks like it's only for Windows? Where would one put this pymolrc.pym file on a Mac? http://www.pymolwiki.org/index.php/Pymolrc On Jan 30, 2013, at 12:12 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Wed, Jan 30, 2013 at 8:33 AM, H. Adam Steinberg a...@steinbergs.us wrote: Is there anyway to change the default settings in PyMol so that when I open the program, it is using my specified defaults? or perhaps there is a way a script can automatically be run at startup? Or automatically run when I fetch in a new pdb? I'm running MacPyMol on 10.8. Yes, just create a file ~/.pymolrc and add whatever settings you want - for instance, this is mine: set auto_zoom = 0 set cartoon_oval_length = 0.8 set cartoon_oval_width = 0.15 set cartoon_rect_length = 0.8 set cartoon_rect_width = 0.15 set ray_shadows = 0 set ray_opaque_background = 0 -Nat H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] default settings
On Wed, Jan 30, 2013 at 10:43 AM, H. Adam Steinberg a...@steinbergs.us wrote: This is great, but looks like it's only for Windows? Where would one put this pymolrc.pym file on a Mac? http://www.pymolwiki.org/index.php/Pymolrc Quoting the wiki: On a linux-type system, this file will be located in /path/to/home/.pymolrc. This should probably be edited to Unix-type system, since Mac and Linux behave identically in this case. -Nat -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] default settings
You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol does try to read it when it starts up. However, it errors every time. If I put just this one command in the file and start up PyMol, it comes back with: File /Users/adam/pymolrc.pym, line 1 set auto_zoom = 0 ^ SyntaxError: invalid syntax On Jan 30, 2013, at 12:46 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Wed, Jan 30, 2013 at 10:43 AM, H. Adam Steinberg a...@steinbergs.us wrote: This is great, but looks like it's only for Windows? Where would one put this pymolrc.pym file on a Mac? http://www.pymolwiki.org/index.php/Pymolrc Quoting the wiki: On a linux-type system, this file will be located in /path/to/home/.pymolrc. This should probably be edited to Unix-type system, since Mac and Linux behave identically in this case. -Nat H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] default settings
On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg a...@steinbergs.us wrote: You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol does try to read it when it starts up. However, it errors every time. If I put just this one command in the file and start up PyMol, it comes back with: File /Users/adam/pymolrc.pym, line 1 set auto_zoom = 0 ^ SyntaxError: invalid syntax That's because you're using the wrong file name: On a linux-type system, this file will be located in /path/to/home/.pymolrc. -Nat -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] default settings
1st, thank you for your patience and help. 2nd, for those who end up trying to also do this… Apple now hides all files in the user folder that start with a period. Therefore, the minute you hit enter after changing the name to .pymolrc, the file disappears. You have to run a third party app that allows you to see the hidden files. I used TinkerTool. This works and solved the problem! Thanks! On Jan 30, 2013, at 12:59 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg a...@steinbergs.us wrote: You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol does try to read it when it starts up. However, it errors every time. If I put just this one command in the file and start up PyMol, it comes back with: File /Users/adam/pymolrc.pym, line 1 set auto_zoom = 0 ^ SyntaxError: invalid syntax That's because you're using the wrong file name: On a linux-type system, this file will be located in /path/to/home/.pymolrc. -Nat H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] default settings
Hi Adam and Nat, a few clarifying remarks on this topic: - The leading dot is optional, so everything that starts with .pymolrc or pymolrc will be found by PyMOL. Files with dot take precedence over files without dot. - Files ending on .py (or .pym) will be parsed as python scripts, files ending on .pml (or .p1m) or without suffix will be parsed as PyMOL command syntax. - Several directories are searched, in order: - $HOME - $HOMEPATH + $HOMEDRIVE (on Windows) - $PYMOL_PATH - PyMOL will even load multiple pymolrc files, however only either with dot or without dot, and only from the same directory. I'll update the PyMOLWiki with that information. A handy script for saving the current set of changed settings to a pymolrc file is available here: http://pymolwiki.org/index.php/Save_settings Cheers, Thomas H. Adam Steinberg wrote, On 01/30/13 20:37: 1st, thank you for your patience and help. 2nd, for those who end up trying to also do this… Apple now hides all files in the user folder that start with a period. Therefore, the minute you hit enter after changing the name to .pymolrc, the file disappears. You have to run a third party app that allows you to see the hidden files. I used TinkerTool. This works and solved the problem! Thanks! On Jan 30, 2013, at 12:59 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg a...@steinbergs.us wrote: You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol does try to read it when it starts up. However, it errors every time. If I put just this one command in the file and start up PyMol, it comes back with: File /Users/adam/pymolrc.pym, line 1 set auto_zoom = 0 ^ SyntaxError: invalid syntax That's because you're using the wrong file name: On a linux-type system, this file will be located in /path/to/home/.pymolrc. -Nat -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
