try running
find ~/ -name “newpdb.pdb” > On Nov 27, 2015, at 9:08 PM, Smith Liu <smith_liu...@163.com> wrote: > > > Dear All, > > Osvaldo is new here for this question, so I repeat it a little. By pymol I > open a pdb and orient it and I want to save the oriented pdb. First I input > command "orient" after load the pdb, then I input command "run > save_trannsforme.py all, newpdb.pdb". I have tried to locate the newpdb.pdb > by locate newpdb.pdb or find newpdb.pdb, even as the root user, but I cannot > find the outpur newpdb.pdb. My pymol is Linux Open-Source PyMOL 1.6.X. > > I am looking forward to getting a reply from you on how to get the oriented > pdb, which should be different from the original PDB I load. > > Smith > > > > > > > At 2015-11-28 00:44:07, "Shane Caldwell" <shane.caldwel...@gmail.com> wrote: > Hi Smith, > > It will be in whatever folder pymol is launched from. If you launched pymol > from a specific place, it will be that folder. If not, it might be in the > system files for pymol, which will depend on your operating system and > architecture. > > Shane > > > Shane Caldwell > McGill University > > On Fri, Nov 27, 2015 at 12:59 AM, Smith Liu <smith_liu...@163.com > <mailto:smith_liu...@163.com>> wrote: > Dear All， > > Once a molecule displayed in pymol, first I input command "orient", then I > input command "run save_trannsforme.py all, newpdb.pdb", I cannot get the > oriented newpdb.pdb. > > Will you please show me how to get the oriented newpdb.pdb? > > Smith > > > > > > At 2015-11-26 18:58:48, "Spencer Bliven" <spencer.bli...@gmail.com > <mailto:spencer.bli...@gmail.com>> wrote: > Smith– > > The code is intended to be saved to a file ("save_transformed.py") and then > loaded into pymol using `run /path/to/save_transformed.py`. There's some > general info on running pymol scripts: Simple_Scripting > <http://pymolwiki.org/index.php/Simple_Scripting> Running_Scripts > <http://pymolwiki.org/index.php/Running_Scripts> > > The script defines a new command which can be run e.g. `save_transformed > <object>, <file>`. You don't have to replace anything in the script yourself. > > Note that the save_transformed command modifies the object it's run on, so > you might want to run it on a backup copy by first calling `create > <object>_backup, <object>` > > -Spencer > > On Thu, Nov 26, 2015 at 8:33 AM, Smith Liu <smith_liu...@163.com > <mailto:smith_liu...@163.com>> wrote: > Dear All, > > For get view, we get something like > > set_view (\ > 0.999876618, -0.000452542, -0.015699286,\ > 0.000446742, 0.999999821, -0.000372844,\ > 0.015699454, 0.000365782, 0.999876678,\ > 0.000000000, 0.000000000, -150.258514404,\ > 11.842411041, 20.648729324, 8.775371552,\ > 118.464958191, 182.052062988, 0.000000000 ) > > For save trasformed pdb file, we need sonething like > > ttt = [m[0], m[1], m[2], 0.0, > m[3], m[4], m[5], 0.0, > m[6], m[7], m[8], 0.0, > 0.0, 0.0, 0.0, 1.0] > Will you please show me how to replace m[0], m[1].... from what we get by > get_view? Which item is which item? > > In addition, for the save_transformed.py, the last sentence is > "cmd.extend('save_transformed',save_transformed)". Should we replace the > second save_transformed with something, for example *.pdb? Ortherwise how to > get the output modified PDB? > > > I am looking forward to getting a reply from you. > > Smith > > > > > > > > > > > > > At 2015-11-26 14:24:15, "Andreas Forster" <docandr...@gmail.com > <mailto:docandr...@gmail.com>> wrote: > http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures > <http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures> > > > Andreas > > > On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu <smith_liu...@163.com > <mailto:smith_liu...@163.com>> wrote: > Dear Shane, > > > get_view is a nice command. Is any way to change the original PDB based on > what we get by set_view to get the new pdb? > > Smith > > > > > > > At 2015-11-26 03:54:32, "Shane Caldwell" <shane.caldwel...@gmail.com > <mailto:shane.caldwel...@gmail.com>> wrote: > Hi Smith, > > You can type > > >get_view > > and copy the output into a txt file for later use. The output set_view > command will return the window to the same camera settings > > Shane > > Shane Caldwell > McGill University > > On Tue, Nov 24, 2015 at 9:45 PM, Smith Liu <smith_liu...@163.com > <mailto:smith_liu...@163.com>> wrote: > Dear All, > > Suppose the original PDB was not oriented. Once we have it oriented by pymol, > is any way we can save the new PDB oriented? > > Smith > > > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 > <http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140> > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net > <mailto:PyMOL-users@lists.sourceforge.net>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > <https://lists.sourceforge.net/lists/listinfo/pymol-users> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> > > > > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 > <http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140> > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net > <mailto:PyMOL-users@lists.sourceforge.net>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > <https://lists.sourceforge.net/lists/listinfo/pymol-users> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> > > > > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 > <http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140> > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net > <mailto:PyMOL-users@lists.sourceforge.net>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > <https://lists.sourceforge.net/lists/listinfo/pymol-users> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > <http://www.mail-archive.com/pymol-users@lists.sourceforge.net> > > > > > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > 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
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